@article{mickelson-young_wear_song_zynda_hanley-bowdoin_thompson_2021, title={A protocol for genome-wide analysis of DNA replication timing in intact root tips}, journal={Methods in Molecular Biology series}, author={Mickelson-Young, Leigh and Wear, Emily E. and Song, Jawon and Zynda, Gregory J. and Hanley-Bowdoin, Linda and Thompson, William F.}, year={2021} }
 @article{borges_donoghue_leblanc_wear_tanurdzic_berube_brooks_thompson_hanley-bowdoin_martienssen_2021, title={Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation}, volume={31}, ISBN={1879-0445}, url={https://doi.org/10.1016/j.cub.2020.10.098}, DOI={10.1016/j.cub.2020.10.098}, abstractNote={5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.}, number={3}, journal={CURRENT BIOLOGY}, publisher={Elsevier BV}, author={Borges, Filipe and Donoghue, Mark T. A. and LeBlanc, Chantal and Wear, Emily E. and Tanurdzic, Milos and Berube, Benjamin and Brooks, Ashley and Thompson, William F. and Hanley-Bowdoin, Linda and Martienssen, Robert A.}, year={2021}, pages={591-+} }
 @article{wheeler_brooks_concia_vera_wear_leblanc_ramu_vaughn_bass_martienssen_et al._2020, title={Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin(1)([OPEN])}, volume={183}, ISSN={["1532-2548"]}, DOI={10.1104/pp.19.01520}, abstractNote={DNA replication initiation sites in plants associate most strongly with AT-rich and highly accessible chromatin, and not with genes or a particular epigenetic signature. The selection and firing of DNA replication origins play key roles in ensuring that eukaryotes accurately replicate their genomes. This process is not well documented in plants due in large measure to difficulties in working with plant systems. We developed a new functional assay to label and map very early replicating loci that must, by definition, include at least a subset of replication origins. Arabidopsis (Arabidopsis thaliana) cells were briefly labeled with 5-ethynyl-2′-deoxy-uridine, and nuclei were subjected to two-parameter flow sorting. We identified more than 5500 loci as initiation regions (IRs), the first regions to replicate in very early S phase. These were classified as strong or weak IRs based on the strength of their replication signals. Strong initiation regions were evenly spaced along chromosomal arms and depleted in centromeres, while weak initiation regions were enriched in centromeric regions. IRs are AT-rich sequences flanked by more GC-rich regions and located predominantly in intergenic regions. Nuclease sensitivity assays indicated that IRs are associated with accessible chromatin. Based on these observations, initiation of plant DNA replication shows some similarity to, but is also distinct from, initiation in other well-studied eukaryotic systems.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Wheeler, Emily and Brooks, Ashley M. and Concia, Lorenzo and Vera, Daniel L. and Wear, Emily E. and LeBlanc, Chantal and Ramu, Umamaheswari and Vaughn, Matthew W. and Bass, Hank W. and Martienssen, Robert A. and et al.}, year={2020}, month={May}, pages={206–220} }
 @article{wear_song_zynda_mickelson-young_leblanc_lee_deppong_allen_martienssen_vaughn_et al._2020, title={Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots}, volume={16}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1008623}, abstractNote={Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.}, number={10}, journal={PLOS GENETICS}, author={Wear, Emily E. and Song, Jawon and Zynda, Gregory J. and Mickelson-Young, Leigh and LeBlanc, Chantal and Lee, Tae-Jin and Deppong, David O. and Allen, George C. and Martienssen, Robert A. and Vaughn, Matthew W. and et al.}, year={2020}, month={Oct} }
 @article{turpin_vera_savadel_lung_wear_mickelson-young_thompson_hanley-bowdoin_dennis_zhang_et al._2018, title={Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L)}, volume={20}, ISSN={["2352-3409"]}, DOI={10.1016/j.dib.2018.08.015}, abstractNote={Presented here are data from Next-Generation Sequencing of differential micrococcal nuclease digestions of formaldehyde-crosslinked chromatin in selected tissues of maize (Zea mays) inbred line B73. Supplemental materials include a wet-bench protocol for making DNS-seq libraries, the DNS-seq data processing pipeline for producing genome browser tracks. This report also includes the peak-calling pipeline using the iSeg algorithm to segment positive and negative peaks from the DNS-seq difference profiles. The data repository for the sequence data is the NCBI SRA, BioProject Accession PRJNA445708.}, journal={DATA IN BRIEF}, author={Turpin, Zachary M. and Vera, Daniel L. and Savadel, Savannah D. and Lung, Pei-Yau and Wear, Emily E. and Mickelson-Young, Leigh and Thompson, William F. and Hanley-Bowdoin, Linda and Dennis, Jonathan H. and Zhang, Jinfeng and et al.}, year={2018}, month={Oct}, pages={358–363} }
 @article{concia_brooks_wheeler_zynda_wear_leblanc_song_lee_pascuzzi_martienssen_et al._2018, title={Genome-Wide Analysis of the Arabidopsis Replication Timing Program}, volume={176}, ISSN={["1532-2548"]}, url={http://europepmc.org/abstract/med/29301956}, DOI={10.1104/pp.17.01537}, abstractNote={The Arabidopsis genome replicates in two noninteracting compartments during early/mid and late S phase. Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2′-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.}, number={3}, journal={PLANT PHYSIOLOGY}, author={Concia, Lorenzo and Brooks, Ashley M. and Wheeler, Emily and Zynda, Gregory J. and Wear, Emily E. and LeBlanc, Chantal and Song, Jawon and Lee, Tae-Jin and Pascuzzi, Pete E. and Martienssen, Robert A. and et al.}, year={2018}, month={Mar}, pages={2166–2185} }
 @article{wear_song_zynda_leblanc_lee_mickelson-young_concia_mulvaney_szymanski_allen_et al._2017, title={Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips}, volume={29}, ISSN={["1532-298X"]}, url={http://europepmc.org/abstract/med/28842533}, DOI={10.1105/tpc.17.00037}, abstractNote={The time during S phase at which different maize DNA sequences replicate reveals a complex temporal program influenced by genomic features, transcriptional activity, and chromatin structure. All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the “Repli-seq” assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.}, number={9}, journal={PLANT CELL}, author={Wear, Emily E. and Song, Jawon and Zynda, Gregory J. and LeBlanc, Chantal and Lee, Tae-Jin and Mickelson-Young, Leigh and Concia, Lorenzo and Mulvaney, Patrick and Szymanski, Eric S. and Allen, George C. and et al.}, year={2017}, month={Sep}, pages={2126–2149} }
 @article{zynda_song_concia_wear_hanley-bowdoin_thompson_vaughn_2017, title={Repliscan: a tool for classifying replication timing regions}, volume={18}, ISSN={["1471-2105"]}, url={http://europepmc.org/abstract/med/28784090}, DOI={10.1186/s12859-017-1774-x}, abstractNote={Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing.To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds.Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.}, journal={BMC BIOINFORMATICS}, author={Zynda, Gregory J. and Song, Jawon and Concia, Lorenzo and Wear, Emily E. and Hanley-Bowdoin, Linda and Thompson, William F. and Vaughn, Matthew W.}, year={2017}, month={Aug}, pages={1–14} }
 @article{mickelson-young_wear_mulvaney_lee_szymanski_allen_hanley-bowdoin_thompson_2016, title={A flow cytometric method for estimating S-phase duration in plants}, volume={67}, ISSN={["1460-2431"]}, url={http://europepmc.org/abstract/med/27697785}, DOI={10.1093/jxb/erw367}, abstractNote={Highlight We estimated S-phase duration for several plant species by following EdU-labeled nuclei from G1 to G2 using bivariate flow cytometry. S-phase duration is relatively consistent over a range of genome sizes.}, number={21}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Mickelson-Young, Leigh and Wear, Emily and Mulvaney, Patrick and Lee, Tae-Jin and Szymanski, Eric S. and Allen, George and Hanley-Bowdoin, Linda and Thompson, William}, year={2016}, month={Nov}, pages={6077–6087} }
 @inbook{wear_concia_brooks_markham_lee_allen_thompson_hanley-bowdoin_2016, title={Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry}, ISBN={9781493931415 9781493931422}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-3142-2_6}, DOI={10.1007/978-1-4939-3142-2_6}, abstractNote={5-Ethynyl-2'-deoxyuridine (EdU) is a nucleoside analog of thymidine that can be rapidly incorporated into replicating DNA in vivo and, subsequently, detected by using "click" chemistry to couple its terminal alkyne group to fluorescent azides such as Alexa Fluor 488. Recently, EdU incorporation followed by coupling with a fluorophore has been used to visualize newly synthesized DNA in a wide range of plant species. One particularly useful application is in flow cytometry, where two-parameter sorting can be employed to analyze different phases of the cell cycle, as defined both by total DNA content and the amount of EdU pulse-labeled DNA. This approach allows analysis of the cell cycle without the need for synchronous cell populations, which can be difficult to obtain in many plant systems. The approach presented here, which was developed for fixed, EdU-labeled nuclei, can be used to prepare analytical profiles as well as to make highly purified preparations of G1, S, or G2/M phase nuclei for molecular or biochemical analysis. We present protocols for EdU pulse labeling, tissue fixation and harvesting, nuclei preparation, and flow sorting. Although developed for Arabidopsis suspension cells and maize root tips, these protocols should be modifiable to many other plant systems.}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Wear, Emily E. and Concia, Lorenzo and Brooks, Ashley M. and Markham, Emily A. and Lee, Tae-Jin and Allen, George C. and Thompson, William F. and Hanley-Bowdoin, Linda}, year={2016}, pages={69–86} }
 @article{bass_hoffman_lee_wear_joseph_allen_hanley-bowdoin_thompson_2015, title={Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei}, volume={89}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-015-0364-4}, abstractNote={Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.}, number={4-5}, journal={PLANT MOLECULAR BIOLOGY}, author={Bass, Hank W. and Hoffman, Gregg G. and Lee, Tae-Jin and Wear, Emily E. and Joseph, Stacey R. and Allen, George C. and Hanley-Bowdoin, Linda and Thompson, William F.}, year={2015}, month={Nov}, pages={339–351} }
 @misc{bass_wear_lee_hoffman_gumber_allen_thompson_hanley-bowdoin_2014, title={A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development}, volume={65}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/ert470}, abstractNote={The progress of nuclear DNA replication is complex in both time and space, and may reflect several levels of chromatin structure and 3-dimensional organization within the nucleus. To understand the relationship between DNA replication and developmental programmes, it is important to examine replication and nuclear substructure in different developmental contexts including natural cell-cycle progressions in situ. Plant meristems offer an ideal opportunity to analyse such processes in the context of normal growth of an organism. Our current understanding of large-scale chromosomal DNA replication has been limited by the lack of appropriate tools to visualize DNA replication with high resolution at defined points within S phase. In this perspective, we discuss a promising new system that can be used to visualize DNA replication in isolated maize (Zea mays L.) root tip nuclei after in planta pulse labelling with the thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Mixed populations of EdU-labelled nuclei are then separated by flow cytometry into sequential stages of S phase and examined directly using 3-dimensional deconvolution microscopy to characterize spatial patterns of plant DNA replication. Combining spatiotemporal analyses with studies of replication and epigenetic inheritance at the molecular level enables an integrated experimental approach to problems of mitotic inheritance and cellular differentiation.}, number={10}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Bass, Hank W. and Wear, Emily E. and Lee, Tae-Jin and Hoffman, Gregg G. and Gumber, Hardeep K. and Allen, George C. and Thompson, William F. and Hanley-Bowdoin, Linda}, year={2014}, month={Jun}, pages={2747–2756} }
 @article{pascuzzi_flores-vergara_lee_sosinski_vaughn_hanley-bowdoin_thompson_allen_2014, title={In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts}, volume={26}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.113.121194}, abstractNote={This work uses tiling microarrays to map S/MARs on Arabidopsis chromosome 4. S/MARs were found to be spaced more closely than in the large plant and animal genomes studied to date and preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation. Most S/MARs occur near gene transcription start sites, and these genes show an increased probability of expression. Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.}, number={1}, journal={PLANT CELL}, author={Pascuzzi, Pete E. and Flores-Vergara, Miguel A. and Lee, Tae-Jin and Sosinski, Bryon and Vaughn, Matthew W. and Hanley-Bowdoin, Linda and Thompson, William F. and Allen, George C.}, year={2014}, month={Jan}, pages={102–120} }
 @article{santa-maria_yencho_haigler_thompson_kelly_sosinski_2011, title={Starch Self-Processing in Transgenic Sweet Potato Roots Expressing a Hyperthermophilic alpha-Amylase}, volume={27}, ISSN={["1520-6033"]}, url={http://europepmc.org/abstract/med/21365786}, DOI={10.1002/btpr.573}, abstractNote={Abstract}, number={2}, journal={BIOTECHNOLOGY PROGRESS}, author={Santa-Maria, Monica C. and Yencho, Craig G. and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2011}, pages={351–359} }
 @article{lee_pascuzzi_settlage_shultz_tanurdzic_rabinowicz_menges_zheng_main_murray_et al._2010, title={Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State}, volume={6}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1000982}, DOI={10.1371/journal.pgen.1000982}, abstractNote={DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins.}, number={6}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Lee, Tae-Jin and Pascuzzi, Pete E. and Settlage, Sharon B. and Shultz, Randall W. and Tanurdzic, Milos and Rabinowicz, Pablo D. and Menges, Margit and Zheng, Ping and Main, Dorrie and Murray, James A. H. and et al.}, editor={Copenhaver, Gregory P.Editor}, year={2010}, month={Jun}, pages={e1000982} }
 @article{shultz_lee_allen_thompson_hanley-bowdoin_2009, title={Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants}, volume={150}, ISSN={["1532-2548"]}, DOI={10.1104/pp.109.136614}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Shultz, Randall W. and Lee, Tae-Jin and Allen, George C. and Thompson, William F. and Hanley-Bowdoin, Linda}, year={2009}, month={Jun}, pages={658–669} }
 @inbook{kumar_thompson_2009, title={Plant Genome Engineering Using Zinc Finger Nucleases}, ISBN={9789048129669 9789048129676}, url={http://dx.doi.org/10.1007/978-90-481-2967-6_24}, DOI={10.1007/978-90-481-2967-6_24}, booktitle={Molecular Techniques in Crop Improvement}, publisher={Springer Netherlands}, author={Kumar, Sandeep and Thompson, William F.}, year={2009}, month={Oct}, pages={579–590} }
 @article{santa-maria_chou_yencho_haigler_thompson_kelly_sosinski_2009, title={Plant cell calcium-rich environment enhances thermostability of recombinantly produced α-amylase from the hyperthermophilic bacterium Thermotoga maritime}, volume={104}, ISSN={0006-3592 1097-0290}, url={http://dx.doi.org/10.1002/bit.22468}, DOI={10.1002/bit.22468}, abstractNote={Abstract}, number={5}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Santa-Maria, Monica C. and Chou, Chung-Jung and Yencho, G. Craig and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2009}, month={Dec}, pages={947–956} }
 @article{kumar_thompson_2009, title={Simultaneous excision of two transgene flanking sequences and resolution of complex integration loci}, volume={69}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-008-9402-9}, abstractNote={In planta excision techniques have proven useful both for basic biology and applied biotechnology. In this report, we describe a simple site-specific recombination (SSR) strategy that simultaneously removes pre-defined DNA sequences from both sides of a transgenic "gene of interest," leaving only the desired gene and short sequences from the recombinase recognition site. We have used the FLP/FRT SSR system to provide a proof of concept, though any of several other SSR systems could be used in the same way. The frequency of double excision ranged from 33% to 83% in different transgenic lines. We show that a single SSR reaction can simultaneously carry out double excisions and resolve complex transgene loci at high frequency. The method has direct biotechnological application and provides a useful tool for basic research.}, number={1-2}, journal={PLANT MOLECULAR BIOLOGY}, author={Kumar, Sandeep and Thompson, William F.}, year={2009}, month={Jan}, pages={23–32} }
 @article{tanurdzic_vaughn_jiang_lee_slotkin_sosinski_thompson_doerge_martienssen_2008, title={Epigenomic Consequences of Immortalized Plant Cell Suspension Culture}, volume={6}, ISSN={1545-7885}, url={http://dx.doi.org/10.1371/journal.pbio.0060302}, DOI={10.1371/journal.pbio.0060302}, abstractNote={Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture.}, number={12}, journal={PLoS Biology}, publisher={Public Library of Science (PLoS)}, author={Tanurdzic, Milos and Vaughn, Matthew W and Jiang, Hongmei and Lee, Tae-Jin and Slotkin, R. Keith and Sosinski, Bryon and Thompson, William F and Doerge, R. W and Martienssen, Robert A}, editor={Reik, WolfEditor}, year={2008}, month={Dec}, pages={e302} }
 @misc{tanurdzic_vaughn_jiang_lee_slotkin_sosinski_thompson_doerge_martienssen_2008, title={Epigenomic consequences of immortalized plant cell suspension culture}, volume={6}, number={12}, journal={PLoS Biology}, author={Tanurdzic, M. and Vaughn, M. W. and Jiang, H. and Lee, T. J. and Slotkin, R. K. and Sosinski, B. and Thompson, W. F. and Doerge, R. W. and Martienssen, R. A.}, year={2008}, pages={2880–2895} }
 @misc{shultz_tatineni_hanley-bowdoin_thompson_2007, title={Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice(1[W][OA])}, volume={144}, number={4}, journal={Plant Physiology}, author={Shultz, R. W. and Tatineni, V. M. and Hanley-Bowdoin, L. and Thompson, W. F.}, year={2007}, pages={1697–1714} }
 @article{allen_flores-vergara_krasnyanski_kumar_thompson_2006, title={A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide}, volume={1}, ISSN={["1750-2799"]}, DOI={10.1038/nprot.2006.384}, abstractNote={We describe a modification of the DNA extraction method, in which cetyltrimethylammonium bromide (CTAB) is used to extract nucleic acids from plant tissues. In contrast to the original method, the modified CTAB procedure is faster, omits the selective precipitation and CsCl gradient steps, uses less expensive and toxic reagents, requires only inexpensive laboratory equipment and is more readily adapted to high-throughput DNA extraction. This protocol yields approximately 5-30 microg of total DNA from 200 mg of tissue fresh weight, depending on plant species and tissue source. It can be completed in as little as 5-6 h.}, number={5}, journal={NATURE PROTOCOLS}, author={Allen, G. C. and Flores-Vergara, M. A. and Krasnyanski, S. and Kumar, S. and Thompson, W. F.}, year={2006}, pages={2320–2325} }
 @misc{kumar_allen_thompson_2006, title={Gene targeting in plants: fingers on the move}, volume={11}, ISSN={["1360-1385"]}, DOI={10.1016/j.tplants.2006.02.002}, abstractNote={Zinc-finger endonucleases (ZFNs) make targeted double-stranded breaks in genomic DNA and, thus, stimulate recombination and repair processes at specific sites. ZFNs can now be harnessed to stimulate homologous recombination and gene targeting in plants, which represents a major step towards modifying the plant genome more precisely. ZFN-mediated gene targeting is likely to become a powerful tool for genome research and genetic engineering.}, number={4}, journal={TRENDS IN PLANT SCIENCE}, author={Kumar, S and Allen, GC and Thompson, WF}, year={2006}, month={Apr}, pages={159–161} }
 @misc{helmer_allen_thompson_2006, title={High efficiency gene targeting in plants}, volume={7,126,041}, number={2006 Oct. 24}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Helmer, G. L. and Allen, G. C. and Thompson, W. F.}, year={2006} }
 @article{santos_wegel_allen_thompson_stoger_shaw_abranches_2006, title={In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research}, volume={2}, DOI={10.1186/1746-4811-2-18}, abstractNote={Abstract}, journal={Plant Methods}, author={Santos, A.P. and Wegel, E. and Allen, G.C. and Thompson, W.F. and Stoger, E. and Shaw, P. and Abranches, R.}, year={2006}, pages={18} }
 @article{shultz_settlage_hanley-bowdoin_thompson_2005, title={A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue}, volume={23}, ISSN={["0735-9640"]}, DOI={10.1007/BF02788888}, number={4}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Shultz, RW and Settlage, SB and Hanley-Bowdoin, L and Thompson, WF}, year={2005}, month={Dec}, pages={405–409} }
 @article{abranches_shultz_thompson_allen_2005, title={Matrix attachment regions and regulated transcription increase and stabilize transgene expression}, volume={3}, ISSN={["1467-7644"]}, DOI={10.1111/j.1467-7652.2005.00144.x}, abstractNote={Summary}, number={5}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Abranches, R and Shultz, RW and Thompson, WF and Allen, GC}, year={2005}, month={Sep}, pages={535–543} }
 @article{levin_thompson_csinos_stephenson_weissinger_2005, title={Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to Tomato Spotted Wilt Virus in transgenic tobacco}, volume={14}, ISSN={["1573-9368"]}, DOI={10.1007/s11248-004-5413-8}, abstractNote={Matrix attachment regions (MARs) are DNA elements that can increase and stabilize transgene expression. We investigated the effect of the RB7 MAR on transgenic virus resistance. Constructs for resistance to tomato spotted wilt virus (TSWV) with and without flanking RB7 MARs were used to transform tobacco and produce homozygous lines. The population with the MAR construct had a significantly higher percentage of TSWV resistant plants in the R1 generation than the nonMAR population. Each resistant line was advanced to the R4 generation, and significantly fewer MAR lines lost resistance over generations compared to the nonMAR population. Lines with TSWV resistance in growth chamber tests were also resistant in field trials. Two lines that were resistant in the R1 generation and susceptible in the R4 were examined in more detail in order to determine if transcriptional silencing of the transgene was occurring in the later generation. Short interfering 21-25 nt RNAs from the transgene that are characteristic of post-transcriptional gene silencing (PTGS) were present in the resistant R1 plants, but not the susceptible R4 plants, indicating that virus resistance was associated with PTGS of the transgene. Loss of resistance was accompanied by an increase in promoter methylation in both lines. In line M41, the transgene was fully silenced at the transcriptional level in the R4 as shown by nuclear run-on assays. In line NM13, transgene transcription and RNA accumulation was still present in the R4 generation, but the level of transcription was not sufficient to trigger PTGS, suggesting that this line may have partial transcriptional silencing. These results are consistent with the concept that MARs may prevent transcriptional silencing.}, number={2}, journal={TRANSGENIC RESEARCH}, author={Levin, JS and Thompson, WF and Csinos, AS and Stephenson, MG and Weissinger, AK}, year={2005}, month={Apr}, pages={193–206} }
 @article{halweg_thompson_spiker_2005, title={The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: A flow cytometric study}, volume={17}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.104.028100}, abstractNote={Many studies in both plant and animal systems have shown that matrix attachment regions (MARs) can increase expression of transgenes in whole organisms or cells in culture. Because histochemical assays often indicate variegated transgene expression, a question arises: Do MARs increase transgene expression by increasing the percentage of cells expressing the transgene (likelihood), by increasing the level of expression in expressing cells (magnitude), or both? To address this question, we used flow cytometry to measure green fluorescent protein (GFP) expression in individual tobacco (Nicotiana tabacum) cells from lines transformed by Agrobacterium tumefaciens. We conclude that MAR-mediated overall increases in transgene expression involve both likelihood and magnitude. On average, cell lines transformed with the Rb7 MAR-containing vector expressed GFP at levels 2.0- to 3.7-fold higher than controls. MAR lines had fewer nonexpressing cells than control lines (10% versus 45%), and the magnitude of GFP expression in expressing cells was greater in MAR lines by 1.9- to 2.9-fold. We also show that flow cytometry measurements on cells from isogenic lines are consistent with those from populations of independently transformed cell lines. By obviating the need to establish isogenic lines, this use of flow cytometry could greatly simplify the evaluation of MARs or other sequence elements that affect transgene expression.}, number={2}, journal={PLANT CELL}, author={Halweg, C and Thompson, WF and Spiker, S}, year={2005}, month={Feb}, pages={418–429} }
 @article{lee_shultz_hanley-bowdoin_thompson_2004, title={Establishment of rapidly proliferating rice cell suspension culture and its characterization by fluorescence-activated cell sorting analysis}, volume={22}, ISSN={["1572-9818"]}, DOI={10.1007/BF02773136}, number={3}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Lee, TJ and Shultz, RW and Hanley-Bowdoin, L and Thompson, WF}, year={2004}, month={Sep}, pages={259–267} }
 @inbook{allen_spiker_thompson_2004, title={Transgene Integration: Use of Matrix Attachment Regions}, ISBN={1592598277}, url={http://dx.doi.org/10.1385/1-59259-827-7:313}, DOI={10.1385/1-59259-827-7:313}, abstractNote={Matrix attachment regions (MARs) are operationally defined as DNA elements that bind specifically to the nuclear matrix in vitro. When MARs are positioned at the 5′- and 3′-ends of a transgene higher more predictable expression of the transgene results. MARs are increasingly being applied to prevent unwanted transgene silencing, which is especially common when direct DNA transformation methods are used. This chapter describes methods for the isolation of MARs and the subsequent methods allowing the investigator to incorporate MARS into transformation strategies that can both improve transformation frequency and result in predictable, stable expression of the transgenic trait.}, booktitle={Transgenic Plants}, publisher={Humana Press}, author={Allen, George C. and Spiker, Steven and Thompson, William F.}, year={2004}, month={Aug}, pages={313–326} }
 @article{ascenzi_ulker_todd_sowinski_schimeneck_allen_weissinger_thompson_2003, title={Analysis of trans-silencing interactions using transcriptional silencers of varying strength and targets with and without flanking nuclear matrix attachment regions}, volume={12}, ISSN={["1573-9368"]}, DOI={10.1023/A:1023310118231}, abstractNote={We investigated the effect of the Rb7 matrix attachment region (MAR) on trans-silencing in tobacco plants, comparing the effects of three transgene silencer loci on ten target loci. Two of the silencer loci, C40 and C190, contain complex and rearranged transgene arrays consisting of 35S:GUS or NOS:NPTII containing plasmids. The third silencer locus, V271, was previously characterized as a complex locus containing rearranged 35S:RiN sequences. Each of these silencers can reduce 35S promoter-driven expression at other loci, albeit with varying efficiencies. The presence of MARs at a target locus does not prevent trans-silencing by the V271 silencer. However, four of seven MAR-containing loci were at least partially resistant to silencing by the C40 and C190 loci. One MAR locus was unaffected by C40, our weakest silencer, and three were silenced only when the silencer locus was maternally inherited. Silencing is progressive in the F1 and F2 generations; two days after germination there is little or no difference between seedlings derived from crosses to silencing or control lines, but seedlings containing silencer loci slowly lose expression during subsequent development. These observations are compatible with the hypothesis that a product of the silencer locus must accumulate before unlinked loci can be affected. However, our silencer loci are themselves silenced for GUS transcription, and coding region homology is not required for their effects on target loci. Our results are consistent with a model in which transcriptional silencing is triggered by transcription of sequences during the early stages of embryo or seedling development.}, number={3}, journal={TRANSGENIC RESEARCH}, author={Ascenzi, R and Ulker, B and Todd, JJ and Sowinski, DA and Schimeneck, CR and Allen, GC and Weissinger, AK and Thompson, WF}, year={2003}, month={Jun}, pages={305–318} }
 @article{mankin_allen_phelan_spiker_thompson_2003, title={Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3 ' MAR}, volume={12}, ISSN={["0962-8819"]}, DOI={10.1023/A:1022194120518}, abstractNote={We have analyzed effects of a matrix attachment region (MAR) from the tobacco RB7 gene on transgene expression from six different promoters in stably transformed tobacco cell cultures. The presence of MARs flanking the transgene increased expression of constructs based on the constitutive CaMV 35S, NOS, and OCS promoters. Expression from an induced heat shock promoter was also increased and MARs did not cause expression in the absence of heat shock. There was also no effect of MARs on the pea ferredoxin promoter, which is not normally expressed in this cell line. Importantly, most transgenes flanked by RB7 MAR elements showed a large reduction in the number of low expressing GUS transformants relative to control constructs without MARs.}, number={1}, journal={TRANSGENIC RESEARCH}, author={Mankin, SL and Allen, GC and Phelan, T and Spiker, S and Thompson, WF}, year={2003}, month={Feb}, pages={3–12} }
 @article{love_allen_gatz_thompson_2002, title={Differential Top10 promoter regulation by six tetracycline analogues in plant cells}, volume={53}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erf050}, abstractNote={The effects of five tetracycline analogues, anhydrotetracycline, doxycycline, minocycline, oxytetracycline, and tetracycline, on Top10 promoter activity in NT1 tobacco tissue culture cells have been analysed. The concentration that repressed Top10 promoter activity, the level of transgene repression and the kinetics of transgene de-repression were determined for each analogue, and could not be predicted from in vitro binding affinity to the tetracycline repressor or from comparison with animal cells. Doxycycline had the most potent effect on the Top10 promoter and completely inhibited transgene expression at 4 nmol l(-1). Tetracycline was the most versatile of the analogues tested; tetracycline inhibited the Top10 promoter at 10 nmol l(-1) and was easily washed out to restore Top10-driven expression in 12-24 h. A study was also made of the suitability for plant research of a novel tetracycline analogue, GR33076X. In animal cells, GR33076X de-repressed Top10 promoter activity in the presence of inhibitory concentrations of anhydrotetracycline. In NT1, it is shown that GR 33076X can antagonize repression of the Top10 promoter in the presence of tetracycline, but not of anhydrotetracycline or of doxycycline. Different tetracycline analogues can therefore be used to regulate the Top10 promoter in plant cells and this property may be exploited in planning an optimum course of transgene regulation.}, number={376}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Love, J and Allen, GC and Gatz, C and Thompson, WF}, year={2002}, month={Sep}, pages={1871–1877} }
 @article{callaway_abranches_scroggs_allen_thompson_2002, title={High-throughput transgene copy number estimation by competitive PCR}, volume={20}, ISSN={["0735-9640"]}, DOI={10.1007/BF02782462}, number={3}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Callaway, AS and Abranches, R and Scroggs, J and Allen, GC and Thompson, WF}, year={2002}, month={Sep}, pages={265–277} }
 @article{perera_love_heilmann_thompson_boss_2002, title={Up-regulation of phosphoinositide metabolism in tobacco cells constitutively expressing the human type I inositol polyphosphate 5-phosphatase}, volume={129}, ISSN={["1532-2548"]}, DOI={10.1104/pp.003426}, abstractNote={Abstract}, number={4}, journal={PLANT PHYSIOLOGY}, author={Perera, IY and Love, J and Heilmann, I and Thompson, WF and Boss, WF}, year={2002}, month={Aug}, pages={1795–1806} }
 @article{persson_love_tsou_robertson_thompson_boss_2002, title={When a day makes a difference. Interpreting data from endoplasmic reticulum-targeted green fluorescent protein fusions in cells grown in suspension culture}, volume={128}, ISSN={1532-2548 0032-0889}, url={http://dx.doi.org/10.1104/pp.010840}, DOI={10.1104/pp.010840}, abstractNote={The stability of the self-contained structure of green fluorescent protein (GFP) has made it the most widely utilized fluorescent marker for gene expression and subcellular localization studies ([Chalfie et al., 1994][1]; [Tsien, 1998][2]; [De Giorgi et al., 1999][3]; [Haseloff et al., 1999][4]).}, number={2}, journal={Plant Physiology}, publisher={Oxford University Press (OUP)}, author={Persson, S. and Love, J. and Tsou, P. L. and Robertson, D. and Thompson, W. F. and Boss, W. F.}, year={2002}, pages={341–344} }
 @article{mankin_thompson_2001, title={Generation of Intron-Containing, ER-Localized, Soluble-Modified Green Fluorescent Protein Genes for use in Plant Transformation}, volume={19}, DOI={10.1007/bf02824074}, number={1}, journal={Plant Molecular Biology Reporter}, author={Mankin, S.L. and Thompson, W.F.}, year={2001}, pages={13–26} }
 @misc{thompson_2001, title={Method for reducing expression variability of transgenes in plant cells}, volume={6,239,328}, number={2001 May 29}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Thompson, W. F.}, year={2001} }
 @article{hansen_petracek_dickey_thompson_2001, title={The 5 ' end of the pea ferredoxin-1 mRNA mediates rapid and reversible light-directed changes in translation in tobacco}, volume={125}, ISSN={["0032-0889"]}, DOI={10.1104/pp.125.2.770}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Hansen, ER and Petracek, ME and Dickey, LF and Thompson, WF}, year={2001}, month={Feb}, pages={770–778} }
 @article{persson_wyatt_love_thompson_robertson_boss_2001, title={The Ca2+ status of the endoplasmic reticulum is altered by induction of calreticulin expression in transgenic plants}, volume={126}, ISSN={["1532-2548"]}, DOI={10.1104/pp.126.3.1092}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Persson, S and Wyatt, SE and Love, J and Thompson, WF and Robertson, D and Boss, WF}, year={2001}, month={Jul}, pages={1092–1104} }
 @article{ascenzi_ingram_massel_thompson_spiker_weissinger_2001, title={The role of cell differentiation state and HMG-I/Y in the expression of transgenes flanked by matrix attachment regions}, volume={10}, ISSN={["0962-8819"]}, DOI={10.1023/A:1012082602587}, abstractNote={The tobacco nuclear matrix attachment region (MAR), RB7, has been shown to have a much greater effect on transgene expression in cultured cells than in transgenic plants. This is comparable to work in mouse systems showing that MARs have a positive effect on transgene expression in embryonic tissues but not adult tissues. There are several possible explanations for these observations. One is that cell differentiation state and proliferation rate can affect MAR function. We tested this possibility by initiating suspension cell cultures from well-characterized transgenic plants transformed with 35S::GUS with and without flanking MARs and then comparing GUS specific activity in the cell lines to those of the transgenic plants from which the cell lines were derived. If cell differentiation state and proliferation rate do affect MAR function, we would expect the ratio of transgene expression (cell suspensions : plants) to be greater in MAR lines than in control lines. This turned out not to be the case. Thus, it appears that MAR function is not enhanced simply because cells in culture divide rapidly and are not differentiated. Because in animal systems the chromosomal protein HMG-I/Y has been shown to be upregulated in proliferating cells and may have a role in MAR function, we have also examined the levels of the tobacco HMG-I/Y homolog by immunoblotting. The level of this protein does not differ between primary transformant cultured cells (NT-1) and Nicotiana tabacum plants (SR-1). However, a higher molecular weight cross-reacting polypeptide was found in nuclei from the NT-1 cell suspensions but was not detected in SR-1 leaf nuclei or cell suspensions derived from the SR-1 plants.}, number={5}, journal={TRANSGENIC RESEARCH}, author={Ascenzi, R and Ingram, JL and Massel, M and Thompson, WF and Spiker, S and Weissinger, AK}, year={2001}, pages={465–470} }
 @article{ling_wells_tanguay_dickey_thompson_gallie_2000, title={Heat shock protein HSP101 binds to the Fed-1 internal light regulatory element and mediates its high translational activity}, volume={12}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.12.7.1213}, abstractNote={The internal light-regulatory element (iLRE) of ferredoxin (Fed-1) mRNA, comprising the 5′ leader and at least the first 13 codons of the open reading frame, controls transcript abundance after illumination of the plant in a translation-dependent manner. We have characterized the RNA binding activities associated with the Fed-1 iLRE and have identified one activity as the heat shock protein HSP101, a protein shown to bind the 5′ leader of tobacco mosaic virus. HSP101 was sufficient and necessary to mediate a high level of translational activity from a Fed-1 iLRE-containing mRNA in yeast. Moreover, the Fed-1 iLRE substantially enhanced translation of reporter mRNAs in plant protoplasts expressing HSP101. Expression of HSP101 was subject to developmental regulation in leaves in that expression was highest in young leaves. These data suggest that Fed-1 mRNA may use the HSP101 regulatory mechanism as a means of ensuring a high level of translation required for the light-mediated regulation of Fed-1 mRNA stability.}, number={7}, journal={PLANT CELL}, author={Ling, J and Wells, DR and Tanguay, RL and Dickey, LF and Thompson, WF and Gallie, DR}, year={2000}, month={Jul}, pages={1213–1227} }
 @misc{thompson_allen_mankin_2000, title={Increasing expression of transgenes in plant cells using insulator elements}, volume={6,100,448}, number={2000 Aug. 8}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Thompson, W. and Allen, G. and Mankin, S.}, year={2000} }
 @misc{thompson_allen_mankin_2000, title={Method for reducing expression variability of transgenes in plant cells}, volume={6,037,525}, number={2000 Mar. 14}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Thompson, W. and Allen, G. and Mankin, S.}, year={2000} }
 @inbook{petracek_thompson_2000, title={Post-Transcriptional Light Regulation of Nuclear-Encoded Genes}, ISBN={9781461368847 9781461541998}, url={http://dx.doi.org/10.1007/978-1-4615-4199-8_1}, DOI={10.1007/978-1-4615-4199-8_1}, abstractNote={A significant number of studies have detected a post-transcriptional component in the light responses of nuclear genes. As yet there are few in-depth studies of the mechanism(s) involved, and it seems likely some additional examples have been missed. For instance, transcriptional responses have sometimes been inferred on the basis of experiments with translational fusions containing both the promoter and 5' UTR of the test gene, but we now know that elements within the 5' UTR can mediate post-transcriptional light responses. Similarly, because of possible changes in translation rates and protein turnover, the common assumption that mRNA levels directly dictate protein levels is tenuous at best. It is no longer permissible to assume that the biological effect of a gene is a simple function of its transcription. Thus it is likely that with careful experimental design, reports of nuclear-encoded post-transcriptional gene regulation will become increasingly prevalent.}, booktitle={Genetic Engineering}, publisher={Springer US}, author={Petracek, Marie E. and Thompson, W. F.}, year={2000}, pages={1–10} }
 @article{petracek_nuygen_thompson_dickey_2000, title={Premature termination codons destabilize ferredoxin-1 mRNA when ferredoxin-1 is translated}, volume={21}, ISSN={["1365-313X"]}, DOI={10.1046/j.1365-313x.2000.00705.x}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Petracek, ME and Nuygen, T and Thompson, WF and Dickey, LF}, year={2000}, month={Mar}, pages={563–569} }
 @article{love_scott_thompson_2000, title={Stringent control of transgene expression in Arabidopsis thaliana using the Top10 promoter system}, volume={21}, ISSN={["0960-7412"]}, DOI={10.1046/j.1365-313x.2000.00706.x}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Love, J and Scott, AC and Thompson, WF}, year={2000}, month={Mar}, pages={579–588} }
 @misc{allen_spiker_thompson_2000, title={Use of matrix attachment regions (MARs) to minimize transgene silencing}, volume={43}, ISSN={["0167-4412"]}, DOI={10.1023/A:1006424621037}, abstractNote={Matrix attachment regions (MARs) are operationally defined as DNA elements that bind specifically to the nuclear matrix in vitro. It is possible, although unproven, that they also mediate binding of chromatin to the nuclear matrix in vivo and alter the topology of the genome in interphase nuclei. When MARs are positioned on either side of a transgene their presence usually results in higher and more stable expression in transgenic plants or cell lines, most likely by minimizing gene silencing. Our review explores current data and presents several plausible models to explain MAR effects on transgene expression.}, number={2-3}, journal={PLANT MOLECULAR BIOLOGY}, author={Allen, GC and Spiker, S and Thompson, WF}, year={2000}, month={Jun}, pages={361–376} }
 @article{ulker_allen_thompson_spiker_weissinger_1999, title={A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants}, volume={18}, ISSN={["1365-313X"]}, DOI={10.1046/j.1365-313X.1999.00453.x}, abstractNote={Summary}, number={3}, journal={PLANT JOURNAL}, author={Ulker, B and Allen, GC and Thompson, WF and Spiker, S and Weissinger, AK}, year={1999}, month={May}, pages={253–263} }
 @article{michalowski_allen_hall_thompson_spiker_1999, title={Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants}, volume={38}, ISSN={["0006-2960"]}, DOI={10.1021/bi991142c}, abstractNote={Matrix attachment regions (MARs) can be operationally defined as DNA fragments that bind to the nuclear matrix. We have created a library of randomly obtained MARs from tobacco (Nicotiana tobacum) by cloning DNA fragments that co-isolate with nuclear matrixes prepared by a method involving lithium diiodosalicylate. The interactions of several of the cloned MARs with nuclear matrixes were tested by an in vitro binding assay in which genomic DNA was used as competitor. Based on this assay, the MARs were classified as strong, medium, and weak binders. Examples of each of the binding classes were further studied by in vitro binding using self- and cross-competition. Estimates of dissociation constants for several MARs ranged from 6 to 11 nM and correlated inversely with binding strength. The number of binding sites per matrix for several MARs ranged from 4 x 10(5) to 9 x 10(5) and correlated directly with binding strength. We conclude that binding strength, as we have measured it, is a function of both numbers of binding sites and affinity for the sites. The tobacco MARs were sequenced and analyzed for overall AT content, for distribution of AT-rich regions, and for the abundance of several MAR-related motifs. Previously identified MAR motifs correlate to various degrees with binding strength. Notably, the Drosophila topoisomerase II motif does not correlate with binding strength of the tobacco MARs. A newly identified motif, the "90%AT Box," correlates better with binding strength than any of the previously identified motifs we investigated.}, number={39}, journal={BIOCHEMISTRY}, author={Michalowski, SM and Allen, GC and Hall, GE and Thompson, WF and Spiker, S}, year={1999}, month={Sep}, pages={12795–12804} }
 @article{vain_worland_kohli_snape_christou_allen_thompson_1999, title={Matrix attachment regions increase transgene expression levels and stability in transgenic rice plants and their progeny}, volume={18}, ISSN={["0960-7412"]}, DOI={10.1046/j.1365-313X.1999.00446.x}, abstractNote={Summary}, number={3}, journal={PLANT JOURNAL}, author={Vain, P and Worland, B and Kohli, A and Snape, JW and Christou, P and Allen, GC and Thompson, WF}, year={1999}, month={May}, pages={233–242} }
 @article{fitzmaurice_nguyen_wernsman_thompson_conkling_1999, title={Transposon tagging of the sulfur gene of tobacco using engineered maize Ac/Ds elements}, volume={153}, number={4}, journal={Genetics}, author={Fitzmaurice, W. P. and Nguyen, L. V. and Wernsman, E. A. and Thompson, W. F. and Conkling, M. A.}, year={1999}, pages={1919–1928} }
 @article{petracek_dickey_nguyen_gatz_sowinski_allen_thompson_1998, title={Ferredoxin-1 mRNA is destabilized by changes in photosynthetic electron transport}, volume={95}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.95.15.9009}, abstractNote={
            In transgenic tobacco, pea Ferredoxin-1 (
            Fed-1
            ) mRNA accumulates rapidly in response to photosynthesis even when the transgene is driven by a constitutive promoter. To investigate the role of photosynthesis on
            Fed-1
            mRNA stability, we used the tetracycline repressible Top10 promoter system to specifically shut off transcription of the
            Fed-1
            transgene. The
            Fed-1
            mRNA has a half-life of approximately 2.4 hr in the light and a half-life of only 1.2 hr in the dark or in the presence of the photosynthetic electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). These data indicate that cessation of photosynthesis, either by darkness or DCMU results in a destabilization of the
            Fed-1
            mRNA. Furthermore, the
            Fed-1
            mRNA half-life is reduced immediately upon transfer to darkness, suggesting that
            Fed-1
            mRNA destabilization is a primary response to photosynthesis rather than a secondary response to long-term dark adaptation. Finally, the two different methods for efficient tetracycline delivery reported here generally should be useful for half-life measurements of other mRNAs in whole plants.
          }, number={15}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Petracek, ME and Dickey, LF and Nguyen, TT and Gatz, C and Sowinski, DA and Allen, GC and Thompson, WF}, year={1998}, month={Jul}, pages={9009–9013} }
 @article{kjemtrup_sampson_peele_nguyen_conkling_thompson_robertson_1998, title={Gene silencing from plant DNA carried by a Geminivirus}, volume={14}, ISSN={["0960-7412"]}, DOI={10.1046/j.1365-313X.1998.00101.x}, abstractNote={Summary}, number={1}, journal={PLANT JOURNAL}, author={Kjemtrup, S and Sampson, KS and Peele, CG and Nguyen, LV and Conkling, MA and Thompson, WF and Robertson, D}, year={1998}, month={Apr}, pages={91–100} }
 @article{mackerness_liu_thomas_thompson_jordan_white_1998, title={Individual members of the light-harvesting complex II chlorophyll a/b binding protein gene family in pea (Pisum sativum) show differential responses to ultraviolet-B radiation}, volume={103}, DOI={10.1034/j.1399-3054.1998.1030311.x}, abstractNote={Light‐harvesting complex II chlorophyll a/b‐binding protein (Lhcb) mRNA levels are differentially affected by ultraviolet‐B radiation (UV‐B, 280‐320 nm) at different stages of development of pea (Pisum sativum L. cv. Feltham first) seedlings. Addition of UV‐B radiation to the light periods of diurnal cycles of white light resulted in reduction of total Lhcb mRNAs in green leaves but a transient increase in etiolated buds. The aims of this study were to determine the stage during de‐etiolation at which supplementary UV‐B began to inhibit Lhcb gene expression, and to determine whether differential regulation of individual Lhcb genes could explain the differential response to supplementary UV‐B at different developmental stages. All seven Lhcb mRNAs were shown to increase in etiolated buds transferred to a diurnal cycle with supplementary UV‐B during the light periods, but were greatly reduced in green leaves given the same treatment. Therefore, the different responses of total Lhcb mRNA levels to UV‐B radiation in green leaves and etiolated buds are not primarily due to the expression of different members of the Lhcb gene family at different developmental stages. However, the Lhcb genes could be divided into two groups based on their sensitivities to UV‐B. Transcripts from the three genes, Lhcb1*2, Lhcb1*3 and Lhcb1*5, which were undetectable in dark‐grown etiolated buds, exhibited stronger responses to supplementary UV‐B in green leaves than the four genes, Lhcb1*1, Lhcb1*4, Lhcb2*1 and Lhcb3*1, which showed low levels of initial transcript accumulation in dark‐grown etiolated buds. The effect of UV‐B on Lhcb mRNA levels were, however, correlated with chlorophyll content, suggesting that the developmental stage of chloroplasts may be important in determining the responses of the Lhcb genes to supplementary UV‐B radiation in pea seedlings.}, number={3}, journal={Physiologia Plantarum}, author={MacKerness, S. A. H. and Liu, L. S. and Thomas, B. and Thompson, William and Jordan, B. R. and White, M. J.}, year={1998}, pages={377–384} }
 @article{dickey_petracek_nguyen_hansen_thompson_1998, title={Light regulation of Fed-1 mRNA requires an element in the 5' untranslated region and correlates with differential polyribosome association}, volume={10}, DOI={10.2307/3870603}, number={3}, journal={Plant Cell}, author={Dickey, L. F. and Petracek, M. E. and Nguyen, T. T. and Hansen, E. R. and Thompson, William}, year={1998}, pages={475–484} }
 @misc{method of increasing expression for foreign genes in plant cells_1998, volume={5,773,689}, number={1998 June 30}, publisher={Washington, DC: U.S. Patent and Trademark Office}, year={1998} }
 @misc{plant nuclear scaffold attachment region and method for increasing gene expression in transgenic cells_1998, volume={5,773,695}, number={1998 June 30}, publisher={Washington, DC: U.S. Patent and Trademark Office}, year={1998} }
 @inbook{petracek_dickey_hansen_sowinski_nguyen_allen_thompson_1998, title={The dependence of Fed-1 light regulation on translation}, booktitle={A look beyond transcription: Mechanisms determining mRNAstability and translation in plants}, publisher={Washington, DC: American Society of Plant Physiologists}, author={Petracek, M. E. and Dickey, L. F. and Hansen, E. R. and Sowinski, D. A. and Nguyen, T. and Allen, G. C. and Thompson, G. F.}, editor={J. Bailey-Serres and Gallie, D. R.Editors}, year={1998}, pages={96–101} }
 @article{tanzer_thompson_law_wernsman_uknes_1997, title={Characterization of post transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco}, volume={9}, DOI={10.1105/tpc.9.8.1411}, abstractNote={Tobacco lines expressing transgenes that encode tobacco etch virus (TEV) coat protein (CP) mRNA with or without nonsense codons give rise to TEV-resistant tissues that have reduced levels of TEV CP mRNA while maintaining high levels of transgene transcriptional activity. Two phenotypes for virus resistance in the lines containing the transgene have been described: immune (no virus infection) and recovery (initial systemic symptoms followed by gradual recovery over several weeks). Here, we show that at early times in development, immune lines are susceptible to TEV infection and accumulate full-length CP mRNA. Therefore, immune lines also exhibit meiotic resetting, as is seen in the recovery lines, providing molecular evidence for a common mechanism of gene silencing and virus resistance in both cases. We also investigated the characteristics of two sets of low molecular weight RNAs that appear only in silenced tissue. One set has nearly intact 5[prime] ends, lacks poly(A) tails, and is associated with polyribosomes; the second set contains the 3[prime] end of the mRNA. Treating silenced leaf tissue with cycloheximide resulted in decreased levels of full-length mRNA and an increase in the levels of the low molecular weight RNAs, supporting a cytoplasmic decay mechanism that does not require ongoing translation. Surprisingly, mRNA from the transgene containing nonsense codons was associated with more ribosomes than expected, possibly resulting from translation from a start codon downstream of the introduced translational stop codons. We present a hypothesis for transgene/viral RNA degradation in which RNA degradation occurs in the cytoplasm while in association with polyribosomes.}, number={8}, journal={Plant Cell}, author={Tanzer, M. M. and Thompson, William and Law, M. D. and Wernsman, E. A. and Uknes, S.}, year={1997}, pages={1411–1423} }
 @article{mankin_allen_thompson_1997, title={Introduction of a plant intron into the luciferase gene of Photinus pyralis}, volume={15}, DOI={10.1007/bf02812270}, number={2}, journal={Plant Molecular Biology Reporter}, author={Mankin, S. L. and Allen, G. C and Thompson, William}, year={1997}, pages={186–196} }
 @article{petracek_dickey_huber_thompson_1997, title={Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis}, volume={9}, DOI={10.2307/3870586}, number={12}, journal={Plant Cell}, author={Petracek, M. E. and Dickey, L. F. and Huber, S. C. and Thompson, William}, year={1997}, pages={2291–2300} }
 @article{thompson_bevan_wells_shaw_1997, title={Sites of rDNA transcription are widely}, volume={12}, number={1997}, journal={Plant Journal}, author={Thompson, W. F. and Bevan, A. F. and Wells, B. and Shaw, P.}, year={1997}, pages={571–581} }
 @article{frances_thompson_1997, title={The dark-adaptation response of the de-etiolated pea mutant lip1 is modulated by external signals and endogenous programs}, volume={115}, ISSN={["0032-0889"]}, DOI={10.1104/pp.115.1.23}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Frances, S and Thompson, WF}, year={1997}, month={Sep}, pages={23–28} }
 @article{allen_hall_michalowski_newman_spiker_weissinger_thompson_1996, title={High-Level Transgene Expression in Plant Cells: Effects of a Strong Scaffold Attachment Region from Tobacco}, volume={8}, ISSN={1040-4651}, url={http://dx.doi.org/10.2307/3870291}, DOI={10.2307/3870291}, number={5}, journal={The Plant Cell}, publisher={JSTOR}, author={Allen, George C. and Hall, Gerald and Michalowski, Susan and Newman, Winnell and Spiker, Steven and Weissinger, Arthur K. and Thompson, William F.}, year={1996}, month={May}, pages={899} }
 @inbook{thompson_allen_hall_spiker_1996, title={Matrix Attachment Regions and Transgene Expression}, ISBN={9781489902825 9781489902801}, ISSN={1568-1009}, url={http://dx.doi.org/10.1007/978-1-4899-0280-1_16}, DOI={10.1007/978-1-4899-0280-1_16}, abstractNote={Many of the questions we have about how biological systems work are ultimately questions about the regulation of gene expression. For this reason, the control of transcription is fundamental and has received well-deserved attention. From a simplistic point of view, transcription can be though of as being regulated at two levels. The first level (coarse control) involves access of RNA polymerase and transacting factors to the specific DNA sequences with which they interact. Access is a function of chromatin structure. In chromatin fibers of both condensed metaphase chromosomes and interphase chromatin, DNA is highly compacted and essentially inaccessible to RNA polymerase and trans-acting factors. In order to make the DNA accessible, chromatin fibers must in some way take on a more open, less compact structure. Once an open (transcriptionally poised) chromatin structure is obtained, further regulation of transcription involving availability and interactions of transacting factors (fine control), come into play. For reviews see Paranjape et al. (1994) and Reeves (1984).}, booktitle={Genomes of Plants and Animals}, publisher={Springer US}, author={Thompson, William F. and Allen, George C. and Hall, Gerald and Spiker, Steven}, year={1996}, pages={243–269} }
 @article{spiker_thompson_1996, title={Nuclear Matrix Attachment Regions and Transgene Expression in Plants}, volume={110}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.110.1.15}, DOI={10.1104/pp.110.1.15}, abstractNote={DNA sequences called matrix attachment regions (MARs) or scaffold attachment regions (SARs) have recently attracted much attention because of their perceived capacity to increase levels of transgene expression and reduce transformant-to-transformant variation of transgene expression in both plants and animals. Work with these sequences is in its early stages and data that seem to be contradictory have been presented. We do not intend to resolve these controversies here (this will be accomplished by further research). Rather, we will discuss the hypothesized role of MARs in chromatin structure, how MARs are isolated and characterized, what effects MARs have had on the expression of transgenes and the models that have been evoked to explain those effects.}, number={1}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Spiker, S. and Thompson, W. F.}, year={1996}, month={Jan}, pages={15–21} }
 @inbook{petracek_dickey_nguyen_allen_sowinski_hansen_thompson_1996, place={Rockville, MD}, title={Post-transcriptional regulation by light}, booktitle={Regulation of Plant Growth and Development by Light}, publisher={American Society of Plant Physiologists}, author={Petracek, M.E. and Dickey, L.F. and Nguyen, T. and Allen, G.C. and Sowinski, D.A. and Hansen, E.R. and Thompson, W.F.}, editor={Briggs, W.R. and Heath, R.L. and Tobin, E.M.Editors}, year={1996} }
 @inproceedings{thompson_allen_hall_michalowski_newman_spiker_weissinger_1995, title={A nuclear scaffold attachment region from tobacco greatly increases transgene expression in plant cells}, booktitle={Proceedings of the US-Japan Symposium on Modification of Gene Expression and Non-Mendelian Inheritance}, author={Thompson, W.F. and Allen, G.C. and Hall, G. and Michalowski, S. and Newman, W. and Spiker, S. and Weissinger, A.}, editor={Phillips, R. and Oono, K.Editors}, year={1995}, pages={281–295} }
 @article{white_kaufman_horwitz_briggs_thompson_1995, title={Individual Members of the Cab Gene Family Differ Widely in Fluence Response}, volume={107}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.107.1.161}, DOI={10.1104/pp.107.1.161}, abstractNote={Chlorophyll a/b-binding protein genes (Cab genes) can be extremely sensitive to light. Transcript accumulation following a red light pulse increases with fluence over 8 orders of magnitude (L.S. Kaufman, W.F. Thompson, W.R. Briggs [1984] Science 226: 1447–1449). We have constructed fluence-response curves for individual Cab genes. At least two Cab genes (Cab-8 and AB96) show a very low fluence response to a single red light pulse. In contrast, two other Cab genes (AB80 and AB66) fail to produce detectable transcript following a single pulse of either red or blue light but are expressed in continuous red light. Thus, very low fluence responses and high irradiance responses occur in the same gene family.}, number={1}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={White, M. J. and Kaufman, L. S. and Horwitz, B. A. and Briggs, W. R. and Thompson, W. F.}, year={1995}, month={Jan}, pages={161–165} }
 @article{bovy_van den berg_de vrieze_thompson_weisbeek_smeekens_1995, title={Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site}, volume={27}, ISSN={0167-4412 1573-5028}, url={http://dx.doi.org/10.1007/bf00019176}, DOI={10.1007/bf00019176}, abstractNote={The effect of light on the expression of the Arabidopsis thaliana ferredoxin gene (fedA) was studied in mature tobacco plants. In light-treated leaves of tobacco plants transformed with a full-length ferredoxin gene, fedA-specific mRNA levels were more than twenty fold higher than in dark-treated controls. This indicates that all components for regulation of the Arabidopsis ferredoxin gene are present in tobacco. To identify light-regulatory elements in the fedA gene, we have tested a set of chimeric genes containing various parts of the fedA gene for light-dependent expression in mature tobacco plants. A fedA promoter-GUS fusion gene was not light-responsive, indicating that the 5'-upstream promoter region is not sufficient for light regulation. Fusion genes in which different transcribed regions of the fedA gene were expressed from the CaMV 35S promoter showed only limited light regulation, if any at all. This indicates that, like the fedA upstream region, the region downstream of the transcription start site is also not sufficient for full light regulation. The combined results suggest that for full light-regulated expression of the fedA gene, both the promoter region and sequences downstream of the transcription start site are required.}, number={1}, journal={Plant Molecular Biology}, publisher={Springer Nature America, Inc}, author={Bovy, Arnaud and Van Den Berg, Claudia and De Vrieze, Geert and Thompson, William F. and Weisbeek, Peter and Smeekens, Sjef}, year={1995}, month={Jan}, pages={27–39} }
 @article{dickey_nguyen_allen_thompson_1994, title={Light modulation of ferredoxin mRNA abundance requires an open reading frame}, volume={6}, DOI={10.2307/3869894}, journal={Plant Cell}, author={Dickey, L. and Nguyen, F.T.-T. and Allen, G.C. and Thompson, W.F.}, year={1994}, pages={1171–1176} }
 @article{quail_briggs_chory_hangarter_harberd_kendrick_koorneef_parks_sharrock_schäfer_et al._1994, title={Spotlight on phytochrome nomenclature}, volume={6}, DOI={10.2307/3869926}, journal={Plant Cell}, author={Quail, P.H. and Briggs, W.R. and Chory, J. and Hangarter, R.P. and Harberd, N.P. and Kendrick, R.E. and Koorneef, M. and Parks, B. and Sharrock, R.A. and Schäfer, E. and et al.}, year={1994}, pages={468–471} }
 @inbook{dickey_gallo-meagher_thompson_1993, place={Boca Raton, FL}, title={Ferredoxin gene expression and its regulation by light}, booktitle={Control of Plant Gene Expression}, publisher={CRC Press}, author={Dickey, L.F. and Gallo-Meagher, M. and Thompson, W.F.}, editor={Verma, D.P.S.Editor}, year={1993}, pages={211–222} }
 @article{allen_hall_childs_weissinger_spiker_thompson_1993, title={Scaffold attachment regions increase reporter gene expresssion in stably transformed plant cells}, volume={5}, DOI={10.2307/3869803}, number={6}, journal={Plant Cell}, author={Allen, G.C. and Hall, G.E. and Childs, L.C. and Weissinger, A.K. and Spiker, S.L. and Thompson, W.F.}, year={1993}, pages={603–613} }
 @article{falconet_godon_white_thompson_1993, title={Sequence of Lhcb3∗1, a gene encoding a Photosystem II chlorophyll protein in Pisum}, volume={1173}, ISSN={0167-4781}, url={http://dx.doi.org/10.1016/0167-4781(93)90133-x}, DOI={10.1016/0167-4781(93)90133-x}, abstractNote={We have cloned and sequenced a pea Lhcb3 gene, encoding a Photosystem II chlorophyll a/b-binding protein. Sequence analysis indicates that the gene contains two introns and predicts a polypeptide of 265 amino acids. The predicted polypeptide sequence is highly homologous to the polypeptide sequences deduced from Lhcb3 genes previously characterized in tomato and barley.}, number={3}, journal={Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression}, publisher={Elsevier BV}, author={Falconet, Denis and Godon, Christian and White, Michael J. and Thompson, William F.}, year={1993}, month={Jun}, pages={333–336} }
 @article{gallo-meagher_sowinski_elliott_thompson_1992, title={Both internal and external elements control expression of the pea Fed-1 gene in etiolated seedlings}, volume={4}, DOI={10.2307/3869441}, journal={Plant Cell}, author={Gallo-Meagher, M. and Sowinski, D.A. and Elliott, R.C. and Thompson, W.F.}, year={1992}, month={Apr}, pages={389–395} }
 @article{fitzmaurice_lehman_nguyen_thompson_wernsman_conkling_1992, title={Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac}, volume={20}, ISSN={0167-4412 1573-5028}, url={http://dx.doi.org/10.1007/bf00014487}, DOI={10.1007/bf00014487}, abstractNote={This report describes a series of transposon tagging vectors for dicotyledonous plants based on the maize transposable element Ac. This binary system includes the transposase (Ts) and the tagging element (Ds) on separate T-DNA vectors. Ts elements include versions in which transcription is driven either by the endogenous Ac promoter or by the cauliflower mosaic virus (CaMV) 35S promoter. Ds tagging element includes a gene conferring methotrexate (Mtx) resistance for selection and a supF gene to facilitate cloning of tagged sequences. The Ds element is flanked by a CaMV 35S promoter and the beta-glucuronidase (GUS) coding sequence so that GUS expression occurs upon excision of the element. We have transformed these Ts and Ds elements into tobacco and demonstrated that the Ts is functional with either promoter, and that the artificial Ds elements are capable of transposition. The amount of excision was found to depend upon both the individual Ts and Ds primary transformants used. Somatic excision of Ds was seen in up to 100% of progeny seedlings containing Ts and Ds. Germinal excision was detected in up to 48% of the progeny of plants containing both elements. Hence, this system can generate a sufficient number of events to be useful in gene tagging.}, number={2}, journal={Plant Molecular Biology}, publisher={Springer Nature}, author={Fitzmaurice, Wayne P. and Lehman, Lori J. and Nguyen, Long V. and Thompson, William F. and Wernsman, Earl A. and Conkling, Mark A.}, year={1992}, month={Oct}, pages={177–198} }
 @article{white_fristensky_falconet_childs_watson_alexander_roe_thompson_1992, title={Expression of the chlorophyll-a/b-protein multigene family in pea (Pisum sativum L.)}, volume={188}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/bf00216813}, DOI={10.1007/bf00216813}, abstractNote={To measure transcript levels for individual members of the Cab (chlorophyll a/b protein) multigene family in pea under a range of developmental situations, we developed a system using cDNA synthesis, the polymerase chain reaction (PCR), and chemiluminescence detection. In order to design gene-specific PCR primers for all genes, a partial genomic clone for a fifth, Type I LHCII (light-harvesting complex of photosystem II) gene, Cab-9 The Cab-9 sequence appears in the Genbank/EMBL databases under the accession number M86906 , was isolated and sequenced. All seven known Cab genes in pea are expressed in light-grown buds and leaves, including several genes previously known only from genomic clones. There appear to be at least two groups of Cab genes in pea which differ in their response to light and development. The first group (consisting of Cab-8, AB96, Cab-215 and Cab-315) includes Type I, Type II and Type III genes, shows a relatively strong response to red light, and has bud transcript levels similar to or slightly higher than leaves. The second group, consisting of the Type I genes Cab-9, AB80 and AB66, shows little or no transcript accumulation 24 h after a red light pulse, and has higher transcript levels in leaves than in buds. Transcript levels for genes in this second group appear to be lower than those of the first group in all developmental situations examined. These data indicate that there has been an evolutionary divergence of the responses to light and development among the Type I LHCII genes.}, number={2}, journal={Planta}, publisher={Springer Nature America, Inc}, author={White, MichaelJ. and Fristensky, BrianW. and Falconet, Denis and Childs, LisaC. and Watson, JohnC. and Alexander, Laura and Roe, BruceA. and Thompson, WilliamF.}, year={1992}, month={Sep}, pages={190–198} }
 @inbook{dickey_gallo-meagher_thompson_1992, title={Ferredoxin gene expression and its regulation by light}, booktitle={Control of Gene Expression }, publisher={CRC Press}, author={Dickey, L.F. and Gallo-Meagher, M. and Thompson, W.F.}, editor={Verma, D.P.S.Editor}, year={1992}, pages={211–222} }
 @article{frances_white_edgerton_jones_elliott_thompson_1992, title={Initial characterization of a pea mutant with light-independent photomorphogenesis}, volume={4}, DOI={10.2307/3869495}, number={12}, journal={Plant Cell}, author={Frances, S. and White, M.J. and Edgerton, M.D. and Jones, A.M. and Elliott, R.C. and Thompson, W.F.}, year={1992}, month={Dec}, pages={1519–1530} }
 @article{dickey_gallo-meagher_thompson_1992, title={Light regulatory sequences are located within the 5' portion of the Fed-1 message sequence}, volume={11}, DOI={10.1002/j.1460-2075.1992.tb05290.x}, abstractNote={We have previously shown that element(s) mediating a light‐induced increase in the abundance of Fed‐1 mRNA in the leaves of transgenic tobacco plants are located within the transcribed portion of the gene. As part of an effort to define the mechanism of this effect, we report here that cis‐acting elements capable of mediating a 5‐fold light‐induced increase in the abundance of this mRNA are located within a region comprising the 5′ leader and first third of the Fed‐1 coding sequence. No activity was detected in the 3′ untranslated region of the gene. In a gain‐of‐function assay, the 5′ region was found to be capable of conferring light responsiveness on three different reporter sequences, although experiments with the gusA reporter were complicated by an apparent negative light effect on the stability of this mRNA. Deletion experiments show that at least one essential light regulatory element is located in the 5′ untranslated region of Fed‐1 between nucleotides +19 and +57. Additional Fed‐1 sequences, including a portion of the protein coding region, are required to confer positive responsiveness on the gusA reporter. These additional sequences may include specific light regulatory elements or simply provide an environment in which the leader element can function normally.}, number={6}, journal={EMBO Journal}, author={Dickey, L.F. and Gallo-Meagher, M. and Thompson, W.F.}, year={1992}, month={Jun}, pages={2311–2317} }
 @article{gallo-meagher_sowinski_thompson_1992, title={The pea ferredoxin I gene exhibits different light responses in etiolated seedlings of pea and tobacco}, volume={4}, DOI={10.2307/3869440}, journal={Plant Cell}, author={Gallo-Meagher, M. and Sowinski, D.A. and Thompson, W.F.}, year={1992}, month={Apr}, pages={383–388} }
 @article{white_fristensky_thompson_1991, title={Concatemer chain reaction: A taq DNA polymerase-mediated mechanism for generating long tandemly repetitive DNA sequences}, volume={199}, ISSN={0003-2697}, url={http://dx.doi.org/10.1016/0003-2697(91)90087-a}, DOI={10.1016/0003-2697(91)90087-a}, abstractNote={The concatemer chain reaction (CCR) uses Taq DNA polymerase to synthesize double- or single-stranded DNA concatemers whose length and yield can be controlled by varying the number of thermal cycling steps. Although the reactions which occur in CCR are slower and more complex than in polymerase chain reaction (PCR), the practical application of the CCR technique is simple. The CCR technique is less expensive, faster, and easier than conventional methods for producing concatemers and gives greatly improved yields. The templates used in CCR may be: (i) double-stranded concatemer templates produced by ligation, (ii) double-stranded concatemers from previous CCRs, or (iii) single-stranded oligonucleotides consisting of one copy of the sense strand repeat and a complementary but overlapping repeat for the antisense strand. Different molar ratios and lengths (masses) of the two strands of the helix may be obtained. We have used both single-stranded and double-stranded concatemers as targets for RNA hybridization. Applications of this concatemer technology are discussed, including the use of concatemers as hybridization probes or targets in applications such as run-on transcription or analysis of repetitive DNA sequences.}, number={2}, journal={Analytical Biochemistry}, publisher={Elsevier BV}, author={White, Michael J. and Fristensky, Brian W. and Thompson, William F.}, year={1991}, month={Dec}, pages={184–190} }
 @article{pedersen_arwood_spiker_guiltinan_thompson_1991, title={High mobility group chromosomal proteins bind to AT-rich tracts flanking plant genes}, volume={16}, ISSN={0167-4412 1573-5028}, url={http://dx.doi.org/10.1007/bf00017920}, DOI={10.1007/bf00017920}, abstractNote={AT-rich sequences in the 5' flanking regions of several plant genes have been shown to bind nuclear proteins, but the nature of these proteins has remained largely unknown. We report here that certain plant high mobility group (HMG) chromosomal proteins can interact specifically (in the presence of excess non-specific competitor) with AT-rich sequences located upstream of the pea ferredoxin 1 gene (Fed-1) and a member of the wheat Em gene family. Binding was observed with highly purified preparations of HMGa or HMGb, but not with HMGc or HMGd. HMG-DNA complexes were similar to one of the two types of Fed-1 complexes we observed previously using pea nuclear extracts [7]. HMG binding to the Fed-1 DNA was localized to a region containing AT-rich sequences; very similar sequences are present 5' to Em and several other plants genes. Such sequences have been shown to bind unidentified nuclear proteins in a number of these systems. Binding experiments with a synthetic oligo (dA).oligo (dT) probe and competition experiments with synthetic DNA polymers suggest that HMG binding may depend upon structural features of AT-rich DNA rather than being sequence-specific. We discuss the implications of these findings and suggest a role for HMG binding which is consistent with previous evidence linking HMGs with transcriptionally competent chromatin.}, number={1}, journal={Plant Molecular Biology}, publisher={Springer Nature America, Inc}, author={Pedersen, Thomas J. and Arwood, Laura J. and Spiker, Steven and Guiltinan, Mark J. and Thompson, William F.}, year={1991}, month={Jan}, pages={95–104} }
 @article{coleman_thompson_goff_1991, title={Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica}, volume={38}, DOI={10.1111/j.1550-7408.1991.tb06032.x}, abstractNote={ABSTRACT.  Analysis of total DNA isolated from the Chrysophyte alga Ochromonas danica revealed, in addition to nuclear DNA, two genomes present as numerous copies per cell. The larger genome (˜120 kilobase pairs or kbp) is the plastid DNA, which is identified by its hybridization to plasmids containing sequences for the photosynthesis genes rbcL, psbA, and psbC. The smaller genome (40 kbp) is the mitochondrial genome as identified by its hybridization with plasmids containing gene sequences of plant cytochrome oxidase subunits I and II. Both the 120‐ and 40‐kbp genomes contain genes for the small and large subunits of rDNA. The mitochondrial genome is linear with terminal inverted repeats of about 1.6 kbp. Two other morphologically similar species were examined, Ochromonas minuta and Poteriochromonas malhamensis. All three species have linear mitochondrial DNA of 40 kbp. Comparisons of endonuclease restriction‐fragment patterns of the mitochondrial and chloroplast DNAs as well as those of their nuclear rDNA repeats failed to reveal any fragment shared by any two of the species. Likewise, no common fragment size was detected by hybridization with plasmids containing heterologous DNA or with total mitochondrial DNA of O. danica; these observations support the taxonomic assignment of these three organisms to different species. The Ochromonas mitochondrial genomes are the first identified in the chlorophyll a/c group of algae. Combining these results with electron microscopic observations of putative mitochondrial genomes reported for other chromophytes and published molecular studies of other algal groups suggests that all classes of eukaryote algae may have mitochondrial genomes < 100 kbp in size, more like other protistans than land plants.}, number={2}, journal={Journal of Protozoology}, author={Coleman, A.W. and Thompson, W.F. and Goff, L.J.}, year={1991}, month={Mar}, pages={129–135} }
 @article{hall_allen_loer_thompson_spiker_1991, title={Nuclear scaffold and scaffold attachment regions (SARs) in higher plants}, volume={88}, DOI={10.1073/pnas.88.20.9320}, abstractNote={DNA in the nuclei of eukaryotic organisms undergoes a hierarchy of folding to be packaged into interphase and metaphase chromosomes. The first level of packaging is the 11-nm nucleosome fiber, which is further coiled into a 30-nm fiber. Evidence from fungal and animal systems reveals the existence of higher order packaging consisting of loops of the 30-nm fibers attached to a proteinaceous nuclear scaffold by an interaction between the scaffold and specific DNA sequences called scaffold-attachment regions (SARs). Support for the ubiquitous nature of such higher order packaging of DNA is presented here by our work with plants. We have isolated scaffolds from tobacco nuclei using buffers containing lithium diiodosalicylate to remove histones and then using restriction enzymes to remove the DNA not closely associated with the scaffold. We have used Southern hybridization to show that the DNA remaining bound to the scaffolds after nuclease digestion includes SARs flanking three root-specific tobacco genes. This assay for SARs is termed the endogenous assay because it identifies genomic sequences as SARs by their endogenous association with the scaffold. Another assay, the exogenous assay, depends upon the ability of scaffolds to specifically bind exogenously added DNA fragments containing SARs. The tobacco scaffolds specifically bind a well-characterized yeast SAR, and cloned DNA fragments derived from the 3'-flanking regions of the root-specific genes are confirmed to contain SARs by this exogenous assay.}, number={20}, journal={Proceedings of the National Academy of Sciences of United States of America}, author={Hall, G. and Allen, G.C. and Loer, D.S. and Thompson, W.F. and Spiker, S.}, year={1991}, pages={9320–9324} }
 @article{falconet_white_fristensky_dobres_thompson_1991, title={Nucleotide sequence ofCab-215, a Type II gene encoding a photosystem II chlorophylla/b-binding protein inPisum}, volume={17}, ISSN={0167-4412 1573-5028}, url={http://dx.doi.org/10.1007/bf00036815}, DOI={10.1007/bf00036815}, number={1}, journal={Plant Molecular Biology}, publisher={Springer Nature America, Inc}, author={Falconet, Denis and White, Michael J. and Fristensky, Brian W. and Dobres, Michael S. and Thompson, William F.}, year={1991}, month={Jul}, pages={135–139} }
 @article{alexander_falconet_fristensky_white_watson_roe_thompson_1991, title={Nucleotide sequence ofCab-8, a new type I gene encoding a chlorophylla/b-binding protein of LHC II inPisum}, volume={17}, ISSN={0167-4412 1573-5028}, url={http://dx.doi.org/10.1007/bf00040649}, DOI={10.1007/bf00040649}, number={3}, journal={Plant Molecular Biology}, publisher={Springer Nature}, author={Alexander, Laura and Falconet, Denis and Fristensky, Brian W. and White, Michael J. and Watson, John C. and Roe, Bruce A. and Thompson, William F.}, year={1991}, month={Sep}, pages={523–526} }
 @misc{thompson_white_1991, title={PHYSIOLOGICAL AND MOLECULAR STUDIES OF LIGHT-REGULATED NUCLEAR GENES IN HIGHER-PLANTS}, volume={42}, ISSN={["1040-2519"]}, DOI={10.1146/annurev.pp.42.060191.002231}, abstractNote={INTRODUCTION .. . . . . . . . . ..... . . .. .... .... .. .. .. . . ......... ... . . . . . ....... .. .. . . ....... 424 Photoreceptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424 Light Responses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428 D IVERSITY OF RESPONSES... . .. . . . . . . . . . . . . . . . . . . . . ....... . . . ...... 429 Etiolated Seedlings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429 Green Plants . .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433 TRANSC RIPTIONAL CONTROLS 433 In Vitro Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433 Transgenic Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435 POSTIRANSCRIPTIONAL CONTROLS . . . . . . . .. . . ... . . . . 437 Comparison of Transcription and mRNA Abundance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438 The Ferredoxin System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439}, journal={ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY}, author={THOMPSON, WF and WHITE, MJ}, year={1991}, pages={423–466} }
 @article{polans_folta_elliott_thompson_1991, title={The Inheritance and Linkage Mapping of Ferredoxin-1 in Pea}, volume={82}, ISSN={1465-7333 0022-1503}, url={http://dx.doi.org/10.1093/oxfordjournals.jhered.a111080}, DOI={10.1093/oxfordjournals.jhered.a111080}, abstractNote={The Inheritance and Linkage Mapping of Ferredoxin-1 in Pea Get access N. O. Polans, N. O. Polans Search for other works by this author on: Oxford Academic PubMed Google Scholar K. M. Folta, K. M. Folta Search for other works by this author on: Oxford Academic PubMed Google Scholar R. C. Elliott, R. C. Elliott Search for other works by this author on: Oxford Academic PubMed Google Scholar W. F. Thompson W. F. Thompson Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 82, Issue 3, May/June 1991, Pages 259–261, https://doi.org/10.1093/oxfordjournals.jhered.a111080 Published: 01 May 1991}, number={3}, journal={Journal of Heredity}, publisher={Oxford University Press (OUP)}, author={Polans, N. O. and Folta, K. M. and Elliott, R. C. and Thompson, W. F.}, year={1991}, month={May}, pages={259–261} }
 @inbook{thompson_elliott_dickey_gallo_pedersen_sowinski_1991, title={Unusual Features of the Light Response System Regulating Ferredoxin Gene Expression}, ISBN={9783642751325 9783642751301}, url={http://dx.doi.org/10.1007/978-3-642-75130-1_14}, DOI={10.1007/978-3-642-75130-1_14}, booktitle={Phytochrome Properties and Biological Action}, publisher={Springer Berlin Heidelberg}, author={Thompson, W. F. and Elliott, R. C. and Dickey, L. F. and Gallo, M. and Pedersen, T. J. and Sowinski, D. A.}, year={1991}, pages={201–216} }
 @article{thompson_elliott_dickey_fristensky_white_1990, title={Light regulated expression of the Fed-1 gene in pea involves cis-acting elements within the transcription unit}, number={20}, journal={Monograph (British Society for Plant Growth Regulation)}, author={Thompson, W. F. and Elliott, R. C. and Dickey, L. F. and Fristensky, B. W. and White, M. J.}, year={1990}, pages={3} }
 @inbook{thompson_elliott_dickey_fristensky_white_1990, title={Light regulated expression of the Fed-1 gene in pea involves cis-acting elements within the transcription unit}, booktitle={British Society for Plant Growth Regulation, Monograph 20, Mechanisms of Plant Perception and Response to Environmental Stimuli}, author={Thompson, W.F. and Elliott, R.C. and Dickey, L.F. and Fristensky, B.R. and White, M.J.}, editor={Thomas, T. and Smith, A.Editors}, year={1990}, pages={3–17} }
 @article{dobres_thompson_1989, title={A developmentally regulated bud specific mRNA sequence in pea has sequence similarity to seed lectins}, volume={89}, DOI={10.1104/pp.89.3.833}, abstractNote={We report a striking example of organ and stage specific gene expression in pea (Pisum sativum L.). We have identified a transcript to a previously isolated cDNA clone, pEA207 (WF Thompson et al. (1983) Planta 158: 487-500) which accumulates in the actively growing bud of the pea plant and is either absent or present at very low levels in the expanded leaves below the bud. The deduced amino acid sequence of pEA207 shows 49% similarity to the phytohemagglutinin lectin sequence of kidney bean (Phaseolus vulgaris) (LM Hoffman, DD Donaldson (1985) EMBO J 4: 883-889) and 37% similarity to that of the major pea seed lectin sequence (TJV Higgins et al. (1983) J Biol Chem 258: 9544-9549). It is also similar to seed lectins from five other legumes. All of the residues directly involved in metal binding by lectins are present in this sequence. We discuss the possibility that pEA207 encodes a sugar binding lectin-like polypeptide associated with the cell walls of actively growing plant cells.}, number={3}, journal={Plant Physiology}, author={Dobres, M.S. and Thompson, W.F.}, year={1989}, month={Mar}, pages={833–838} }
 @article{elliott_pedersen_fristensky_white_dickey_thompson_1989, title={Characterization of a single copy gene encoding ferredoxin I from pea}, volume={1}, journal={The Plant Cell}, author={Elliott, R.C. and Pedersen, T.J. and Fristensky, B. and White, M.J. and Dickey, L.F. and Thompson, W.F.}, year={1989}, pages={681–690} }
 @article{jordan_hopley_thompson_1989, title={Chloroplast gene expression in lettuce grown under different irradiances}, volume={178}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/bf00392528}, DOI={10.1007/bf00392528}, abstractNote={Chloroplast DNA sequences have been used as hybridisation probes to measure the levels of RNA transcripts present in low- and high-light-grown lettuce (Lactuca sativa L.) plants. The transcript levels for rbc L, psa A, psb A and rDNA are not different between these two light regimes. In contrast, transcript levels for atp BE and pet BD are increased in high-light as a proportion of the chloroplast RNA. Three days after transfer from low-light into high-light, increased transcript levels were found for atp BE, although no change was detected for the psa A or psb A transcripts. In addition, young plants in high-light contain twofold more chloroplast RNA per unit chlorophyll than do low-light plants of equivalent age. Therefore, in these young high-light plants the absolute transcript levels per unit chlorophyll are much greater. With increasing leaf age the RNA per chlorophyll becomes similar for both light conditions. These results are discussed in relation to the photoregulation of chloroplast-encoded gene expression.}, number={1}, journal={Planta}, publisher={Springer Nature America, Inc}, author={Jordan, Brian R. and Hopley, John G. and Thompson, William F.}, year={1989}, pages={69–75} }
 @article{elliott_dickey_white_thompson_1989, title={Cis-acting elements for light regulation of pea ferredoxin I gene expression are located within transcribed sequences}, volume={1}, journal={The Plant Cell}, author={Elliott, R.C. and Dickey, L.F. and White, M.J. and Thompson, W.F.}, year={1989}, pages={691–698} }
 @article{woodbury_dobres_thompson_1989, title={The identification and localization of 33 pea chloroplast transcription initiation sites}, volume={16}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/bf00340723}, DOI={10.1007/bf00340723}, abstractNote={We have used a novel approach to produce a comprehensive transcription initiation map of the pea chloroplast genome. Sites were mapped by measuring the ability of DNA probes to protect 5' ends of transcripts that have been capped in vitro. Using this approach, at least 33 probes appear to contain one or more transcription start sites. A more precise location of some of these sites was obtained by hybrid selecting certain of these RNAs and determining their size both before and after RNase treatment. We have found at least one initiation site in front of every chloroplast gene cluster for which appropriate clones were available. In addition, we have found initiation sites within gene clusters previously shown to be co-transcribed. In one such case, we were able to locate a transcription start site for psbC within the coding sequence of psbD.}, number={5-6}, journal={Current Genetics}, publisher={Springer Nature America, Inc}, author={Woodbury, Neal W. and Dobres, Michael and Thompson, William F.}, year={1989}, month={Dec}, pages={433–445} }
 @article{woodbury_roberts_palmer_thompson_1988, title={A transcription map of the pea chloroplast genome}, volume={14}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/bf00405857}, DOI={10.1007/bf00405857}, abstractNote={A set of 53 cloned pea chloroplast DNA fragments representing approximately 90% of the chloroplast genome was used to probe Northern blots of total pea RNA, resulting in a nearly complete chloroplast transcription map. Similar analyses were performed for RNAs extracted from pea seedlings grown under several different light regimes. We have found that at least 85 kb of the 120 by pea chloroplast genome is represented as detectable transcripts. For many regions of the genome, we have detected multiple overlapping transcripts including both small, gene-sized RNAs and large transcripts covering entire gene clusters. All transcripts detected were more abundant (as a fraction of total cellular RNA) in light grown plants than in plants entirely in the dark. However, larger transcripts were generally more abundant in plants that had been exposed to only 24 h of white light (after germination in the dark) than in plants grown in continuous light. This study indicates that chloroplast genes are often grouped into multigene transcriptional units which can be cotranscribed, and that light-stimulated plastid development involves changes in the relative abundance of the overlapping RNAs of different length that result from transcription of these genes or gene clusters.}, number={1}, journal={Current Genetics}, publisher={Springer Nature America, Inc}, author={Woodbury, Neal W. and Roberts, Linda L. and Palmer, Jeffrey D. and Thompson, William F.}, year={1988}, month={Jul}, pages={75–89} }
 @inbook{thompson_flavell_watson_kaufman_1988, place={ Weinheim}, title={Chromatin structure and expression of plant ribosomal RNA genes}, booktitle={Architecture of Eukaryotic Genes}, publisher={VCH Verlagsgesellschaft}, author={Thompson, W.F. and Flavell, R.B. and Watson, J.C. and Kaufman, L.S.}, editor={Kahl, G.Editor}, year={1988}, pages={385–396} }
 @article{flavell_o'dell_thompson_1988, title={Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat}, volume={204}, DOI={10.1016/0022-2836(88)90352-X}, abstractNote={Cytosine methylation has been studied in wheat rRNA genes at nucleolar organizers displaying different activities. The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. It is concluded that cytosine methylation in rDNA is regulated and that the methylation pattern correlates with the transcription potential of an rRNA gene.}, journal={Journal of Molecular Biology}, author={Flavell, R.B. and O'Dell, M. and Thompson, W.F.}, year={1988}, pages={500–534} }
 @article{thompson_flavell_1988, title={DNase I sensitivity of ribosomal RNA Genes in chromatin and nucleolar dominance in wheat}, volume={204}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/0022-2836(88)90353-1}, DOI={10.1016/0022-2836(88)90353-1}, abstractNote={Ribosomal RNA genes at different nucleolar organizer (NOR) loci in hexaploid wheat are expressed at different levels. The degree of expression of a particular organizer depends on the genetic background, especially on the presence of other NOR loci. For example, when chromosome 1U of Aegilops umbellulata is introduced into the hexaploid wheat cultivar “Chinese Spring” the A. umbellulata NOR accounts for most of the nucleolar activity and seems to suppress the activity of the wheat NOR loci. Even in wild-type “Chinese Spring”, the NOR on chromosome 1B is partially dominant to that on chromosome 6B, since the 1B locus is more active in spite of having fewer genes. We have previously shown that these and other examples of nucleolar dominance in wheat are associated with undermethylation of cytosine residues in certain regions of the dominant rDNA. Here, we show that rRNA genes at dominant loci are organized in a chromatin conformation that renders them more sensitive to DNase I digestion than other rRNA genes. In addition, we have mapped several DNase I-hypersensitive sites in the intergenic spacer region of the rDNA repeating unit. Some of these sites are located near the initiation region for the 45 S rRNA precursor, while others are associated with a series of short direct repeats 5′ to the 45 S rRNA initiation site. The results are discussed in terms of a model in which repeated sequences in the wheat intergenic DNA are presumed to function as upstream promoters and transcriptional enhancers similar to those in Xenopus.}, number={3}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Thompson, W.F. and Flavell, R.B.}, year={1988}, month={Dec}, pages={535–548} }
 @article{palmer_osorio_thompson_1988, title={Inversions in legume chloroplast DNAs}, volume={14}, journal={Current Genetics}, author={Palmer, J.D. and Osorio, B.O. and Thompson, W.F.}, year={1988}, pages={65–74} }
 @article{sagar_horwitz_elliott_thompson_briggs_1988, title={Light Effects on Several Chloroplast Components in Norflurazon-Treated Pea Seedlings}, volume={88}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.88.2.340}, DOI={10.1104/pp.88.2.340}, abstractNote={Changes occurring in several chloroplast components during Norflurazon-induced photobleaching of Pisum sativum seedlings were investigated. mRNA steady state levels of the chlorophyll a/b-binding protein of photosystem II, ferredoxin I, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 and pEA207, two other light-responsive genes, were determined during chlorophyll photooxidation. Relative transcription rates were assayed in isolated nuclei. The results illustrate a complex set of interactions regulating expression of the nuclear and chloroplast genomes. Photobleaching was found to affect the expression of the various genes in different ways. While transcript levels of the chlorophyll a/b-binding protein decreased by more than 80% under photooxidative light conditions in carotenoid-deficient peas, levels of ferredoxin, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 mRNAs were reduced by less than 50%. pEA207 mRNA levels, on the other hand, were resistant to the effects of photobleaching. Analyses of chlorophylls a and b and the chlorophyll a/b-binding protein suggest that accumulation of the protein and its mRNA are coordinated with chlorophyll abundance at several steps. In addition to post-transcriptional regulation at the level of mRNA and protein stability, there may exist coordination at the transcriptional stage.}, number={2}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Sagar, A. D. and Horwitz, B. A. and Elliott, R. C. and Thompson, W. F. and Briggs, W. R.}, year={1988}, month={Oct}, pages={340–347} }
 @book{murphy_thompson_1988, place={Englewood Cliffs, NJ}, title={Molecular Plant Development}, publisher={Prentice Hall}, author={Murphy, T.M. and Thompson, W.F.}, year={1988} }
 @article{sagar_briggs_thompson_1988, title={Nuclear-Cytoplasmic Partitioning of Phytochrome-Regulated Transcripts in Pisum sativum}, volume={88}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.88.4.1397}, DOI={10.1104/pp.88.4.1397}, abstractNote={Nuclear and cytoplasmic mRNAs for several phytochrome-regulated genes were examined in Pisum seedlings in order to investigate possible light effects on mRNA partitioning between the nucleus and cytoplasm. Transcripts from each of five light-regulated genes exhibited different responses to a variety of light treatments, but for each transcript we observed a characteristic linear relationship between nuclear and cytoplasmic levels over a wide range of total transcript abundance. Different mRNAs are characterized by different nuclear-cytoplasmic ;partitioning coefficients', indicating that post-transcriptional events play a significant role in regulating the accumulation of these mRNAs during light induction.}, number={4}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Sagar, A. D. and Briggs, W. R. and Thompson, W. F.}, year={1988}, month={Dec}, pages={1397–1402} }
 @inbook{thompson_kaufman_horwitz_sagar_watson_briggs_1988, title={Patterns of phytochrome-induced gene expression in etiolated pea buds}, ISBN={9789401071239 9789400913950}, url={http://dx.doi.org/10.1007/978-94-009-1395-0_18}, DOI={10.1007/978-94-009-1395-0_18}, booktitle={Biomechanisms Regulating Growth and Development}, publisher={Springer Netherlands}, author={Thompson, W. F. and Kaufman, L. S. and Horwitz, B. A. and Sagar, A. D. and Watson, J. C. and Briggs, W. R.}, year={1988}, pages={269–284} }
 @article{thompson_1988, title={Photoregulation: diverse gene responses in greening seedlings}, volume={11}, ISSN={0140-7791 1365-3040}, url={http://dx.doi.org/10.1111/j.1365-3040.1988.tb01355.x}, DOI={10.1111/j.1365-3040.1988.tb01355.x}, abstractNote={Abstract. Light effects on the expression of nuclear genes for plastid proteins and for the 18S, 5.8S and 25S ribosomal RNAs are discussed, together with some recent information concerning the expression of chloroplast genes in developing plastids. Emphasis is given to the diversity of different responses observed with different genes and evidence for light effects at both transcriptional and post‐transcriptional levels.}, number={5}, journal={Plant, Cell and Environment}, publisher={Wiley}, author={Thompson, W. F.}, year={1988}, month={Jul}, pages={319–328} }
 @article{horwitz_thompson_briggs_1988, title={Phytochrome Regulation of Greening in Pisum: Chlorophyll Accumulation and Abundance of mRNA for the Light-Harvesting Chlorophyll a/b Binding Proteins}, volume={86}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.86.1.299}, DOI={10.1104/pp.86.1.299}, abstractNote={A brief pulse of red light eliminates or reduces the lag in chlorophyll accumulation that occurs when dark-grown pea seedlings are transferred to continuous white light. The red light pulse also induces the accumulation of specific mRNAs. We compared time courses, escape from reversal by far-red light, and fluence-response behavior for induction of mRNA for the light-harvesting chlorophyll a/b binding proteins (Cab mRNA) with those for induction of rapid chlorophyll accumulation in seedlings of Pisum sativum cv Alaska. In both cases the time courses of low fluence and very low fluence responses diverged from each other in a similar fashion: the low fluence responses continued to increase for at least 24 hours, while the very low fluence responses reached saturation by 8 to 16 hours. Both responses escaped from reversibility by far-red slowly, approaching the red control level after 16 hours. The fluence-response curve for the Cab mRNA increase, on the other hand, showed threshold and saturation at fluences 10-fold lower than threshold and saturation values for the greening response. Therefore, the level of Cab mRNA, as measured by the presence of sequences hybridizing to a cDNA probe, does not limit the rate of chlorophyll accumulation after transfer of pea seedlings to white light. The Cab mRNA level in the buds of seedlings grown under continuous red light remained high even when the red fluence rate was too low to allow significant greening. In this case also, abundance of Cab mRNA cannot be what limits chlorophyll accumulation.}, number={1}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Horwitz, B. A. and Thompson, W. F. and Briggs, W. R.}, year={1988}, month={Jan}, pages={299–305} }
 @inbook{watson_thompson_1988, place={Orlando FL}, title={Purification and restriction endonuclease analysis of plant nuclear DNA}, booktitle={Methods for Plant Molecular Biology}, publisher={Academic Press}, author={Watson, J.C. and Thompson, W.F.}, editor={Weissbach, A. and Weissbach, H.Editors}, year={1988} }
 @article{dobres_elliot_watson_thompson_1987, title={A phytochrome-regulated transcript encodes ferredoxin in Pisum sativum}, volume={8}, DOI={10.1007/bf00016434}, abstractNote={We have sequenced the pea (cv. Alaska) cDNA clone pEA46 (16) and shown that it codes for ferredoxin I. This clone has previously been shown to correspond to a transcript whose levels are controlled by phytochrome (Kaufman et al. (1985) Plant Physiol. 78: 388-393; Thompson et al. (1983) Planta 158: 487-500).The deduced amino acid sequence includes part of an hydrophobic transit sequence that shows only very limited homology to that of Silene pratensis ferredoxin.Genomic blotting analysis indicates that ferredoxin I is encoded by one or two genes. A genomic clone (4601) has been isolated that contains the ferredoxin gene and at least 14 kb of flanking sequences.}, journal={Plant Molecular Biology}, author={Dobres, M.S. and Elliot, R.C. and Watson, J.C. and Thompson, W.F.}, year={1987}, pages={53–59} }
 @article{palmer_osorio_aldrich_thompson_1987, title={Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements}, volume={11}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/bf00355401}, DOI={10.1007/bf00355401}, abstractNote={We have compared the sequence organization of four previously uncharacterized legume chloroplast DNAs - from alfalfa, lupine, wisteria and subclover — to that of legume chloroplast DNAs that either retain a large, ribosomal RNA-encoding inverted repeat (mung bean) or have deleted one half of this repeat (broad bean). The circular, 126 kilobase pair (kb) alfalfa chloroplast genome, like those of broad bean and pea, lacks any detectable repeated sequences and contains only a single set of ribosomal RNA genes. However, in contrast to broad bean and pea, alfalfa chloroplast DNA is unrearranged (except for the deletion of one segment of the inverted repeat) relative to chloroplast DNA from mung bean. Together with other findings reported here, these results allow us to determine which of the four possible inverted repeat configurations was deleted in the alfalfa-pea-broad bean lineage, and to show how the present-day broad bean genome may have been derived from an alfalfa-like ancestral genome by two major sequence inversions. The 147 kb lupine chloroplast genome contains a 22 kb inverted repeat and has essentially complete colinearity with the mung bean genome. In contrast, the 130 kb wisteria genome has deleted one half of the inverted repeat and appears colinear with the alfalfa genome. The 140 kb subclover genome has been extensively rearranged and contains a family of at least five dispersed repetitive sequence elements, each several hundred by in size; this is the first report of dispersed repeats of this size in a land plant chloroplast genome. We conclude that the inverted repeat has been lost only once among legumes and that this loss occurred prior to all the other rearrangements observed in subclover, broad bean and pea. Of those lineages that lack the inverted repeat, some are stable and unrearranged, other have undergone a moderate amount of rearrangement, while still others have sustained a complex series of rearrangement either with or without major sequence duplications and transpositions.}, number={4}, journal={Current Genetics}, publisher={Springer Nature America, Inc}, author={Palmer, Jeffrey D. and Osorio, Bernardita and Aldrich, Jane and Thompson, William F.}, year={1987}, month={Jan}, pages={275–286} }
 @article{watson_kaufman_thompson_1987, title={Developmental regulation of cytosine methylation in the nuclear ribosomal RNA genes of Pisum sativum}, volume={193}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/0022-2836(87)90622-x}, DOI={10.1016/0022-2836(87)90622-x}, abstractNote={Prominent features of the cytosine methylation pattern of the Pisum sativum nuclear ribosomal RNA genes have been defined. Cytosine methylation within the C-C-G-G sequence was studied using the restriction enzymes HpaII and MspI and gel blot hybridizations of the restriction digests. The extent to which particular features of the methylation pattern change during seedling development has also been determined. Total cellular DNA, purified from defined sections of pea seedlings grown under different lighting conditions, was analyzed with DNA hybridization probes derived from different portions of a cloned member of the nuclear rRNA gene family. By use of an indirect end-labeling technique, a map of 23 cleavable HpaII and/or MspI sites in genomic rDNA was constructed. The map covers about 90% of the rDNA repeat including the entire non-transcribed spacer region and most of the rRNA coding sequences. One notable feature of the map is that the most prominent HpaII site, located about 800 base-pairs upstream from the 5′ end of the mature 18 S rRNA, is cleaved only in one of the two most abundant rDNA length variants (the short variant). With a gel blot assay specific for cleavage at this site, we estimated the HpaII sensitivity of DNA preparations from several stages of pea seedling development. We find that, while methylation is generally low in young seedlings, DNA obtained from the apical buds of pea seedlings is highly methylated. Further, the methylation level of rDNA within the pea bud decreases as the buds are allowed to develop under continuous white light. Our data, taken together with published studies on pea seedling development, indicate that cytosine methylation levels may be related to the regulated expression of the nuclear rRNA genes in pea.}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Watson, John C. and Kaufman, Lon S. and Thompson, William F.}, year={1987}, month={Jan}, pages={15–26} }
 @article{kaufman_watson_thompson_1987, title={Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum}, volume={84}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.84.6.1550}, DOI={10.1073/pnas.84.6.1550}, abstractNote={
            We have examined the rDNA chromatin of
            Pisum sativum
            plants grown with or without exposure to light for the presence of DNase I hypersensitive sites and possible developmental changes in their distribution. Isolated nuclei from pea seedlings were incubated with various concentrations of DNase I. To visualize the hypersensitive sites, DNA purified from these nuclei was restricted and analyzed by gel blot hybridization. We find that several sites exist in both the coding and noncoding regions of rDNA repeating units. Several of the sites in the nontranscribed spacer region are present in the light but are absent in the dark. Conversely, the hypersensitive sites within the mature rRNA coding regions are present in the dark but absent in the light. There are two major length variants of the rRNA genes in
            P. sativum
            var. Alaska. The sites in the nontranscribed spacer region that appear during the light treatment occur only in the shorter of these two length variants in this cultivar.
          }, number={6}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Kaufman, L. S. and Watson, J. C. and Thompson, W. F.}, year={1987}, month={Mar}, pages={1550–1554} }
 @article{spiller_kaufman_thompson_briggs_1987, title={Specific mRNA and rRNA Levels in Greening Pea Leaves during Recovery from Iron Stress}, volume={84}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.84.2.409}, DOI={10.1104/pp.84.2.409}, abstractNote={Hydroponically grown pea seedlings (Pisum sativum L., cv Alaska) were subjected to Fe stress for 10 to 16 days to produce mature chlorotic leaves. Greening was initiated by adding Fe to the nutrient solution. The levels of chlorophylls, chloroplast, and cytoplasmic rRNAs, and specific chloroplast- and nucleus-encoded mRNAs were all significantly lower in leaves developing during iron stress than in nonstressed leaves. In plants greening after addition of Fe, nuclear transcripts encoding chlorophyll a/b-binding protein and the small subunit of ribulose bisphosphate carboxylase/oxygenase increased about 5-fold in abundance following an 18 to 24 hour lag, as did the chloroplast-encoded transcript for the large subunit of the carboxylase/oxygenase. Chloroplast rRNA showed an increase over that in continually stressed control leaves only after a 40 hour lag. The chloroplast-encoded transcript encoding the Q(B)-binding 32 kilodalton polypeptide of Photosystem II showed little change during greening. Chlorophyll itself increased gradually after a lag period of 24 hours, with an increase in chlorophyll a slightly preceding that of chlorophyll b. Kinetic considerations suggest that the changes observed represent a coordinate series of events initiated by readdition of Fe and occurring in parallel. Though accumulation of mRNA for light-harvesting, chlorophyll-a/b-binding protein might limit chlorophyll accumulation at the onset, subsequent changes in the mRNA do not parallel chlorophyll changes. All three of the mRNAs showing recovery on addition of Fe to Fe-stressed plants undergo sharp diurnal fluctuations in abundance. Such fluctuations are comparable to those in nonstressed controls (mRNA for light-harvesting protein) or considerably more pronounced (mRNAs for carboxylase large and small subunits). The carboxylase small subunit mRNA and that for light-harvesting chlorophyll-binding protein were measured under constant conditions of light and temperature. Though a rhythm in greening leaves was hard to detect, it was prominent in the Fe-sufficient controls, persisting undamped through three full cycles for both mRNAs, and hence is probably circadian.}, number={2}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Spiller, S. C. and Kaufman, L. S. and Thompson, W. F. and Briggs, W. R.}, year={1987}, month={Jun}, pages={409–414} }
 @article{jorgensen_cuellar_thompson_1987, title={Structure and variation in ribosomal RNA genes of pea: Characterization of a cloned rDNA repeat and chromosomal rDNA variants}, volume={8}, DOI={10.1007/bf00016429}, abstractNote={A complete ribosomal DNA (rDNA) repeat unit has been cloned from the genome of Pisum sativum (garden pea) and used to construct a map containing a total of 58 cleavage sites for 23 different restriction enzymes. Regions encoding 18s and 25s ribosomal RNA (rRNA) were identified by R-loop analysis. A 180 bp sequence element is repeated eight times in the intergenic 'nontranscribed spacer' (NTS) region, as defined by eight evenly spaced RsaI cleavage sites. Sequence heterogeneity among these elements (subrepeats) is indicated by the presence of an NcoI site within the five RsaI subrepeats distal to the 25s rRNA gene but not in the three subrepeats proximal to this gene, and also by the presence of an additional RsaI cleavage site in one subrepeat.The approximately 4000 copies of the rDNA repeat in the pea nuclear genome show considerable heterogeneity with respect to the length of the NTS region, and differences are also frequently observed between different genotypes. In both cases the length variation appears to be due primarily to differences in the number of subrepeat elements.Comparison of rDNA restriction maps for two pea genotypes separated for hundreds or perhaps thousands of generations reveals that they contain many rDNA identical repeat units. This data is consistent with the view that new rDNA variants are fixed only infrequently in the evolution of a species.Differences also exist between the rDNA repeats of a single genotype with respect to the degree of base modification at certain restriction sites. A large number of sites known to exist in the pea rDNA clone are not cleaved at all in genomic rDNA, or are cleaved in only some copies of the rDNA repeat. We believe these examples of incomplete cleavage results mostly from methylation, although it is difficult to rule out the possibility of sequence variation in all cases. Most putative modifications are best interpreted in terms of cytosine methylation in CG and CXG sequences, but at least one example is more consistent with adenine methylation.We also have constructed a more detailed restriction map of the wheat rDNA clone pTA71 and present a comparison of this map to our map of pea, pumpkin, and wheat in order to assess the amount of useful evolutionary information that can be obtained by comparison of such maps.}, number={1}, journal={Plant Molecular Biology}, author={Jorgensen, R.A. and Cuellar, R.E. and Thompson, W.F.}, year={1987}, pages={3–12} }
 @article{polans_weeden_thompson_1986, title={Distribution, inheritance and linkage relationships of ribosomal DNA spacer length variants in pea}, volume={72}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/bf00288563}, DOI={10.1007/bf00288563}, abstractNote={DNA restriction endonuclease fragment analysis is used to examine the genetic organization, inheritance and linkage associations of the ribosomal DNA in pea. The substantial variation observed in the length of the intergenic spacer region is shown to segregate in Mendelian fashion involving two independent genetic loci, designated Rrn1 and Rrn2. Linkage between Rrn1 and two marker loci on chromosome 4 establishes the approximate location of this tandem array. Rrn2 shows linkage with a set of isozyme loci which assort independently of other markers on all seven chromosomes. Combining these observations with previous cytological data, we suggest that Rrn2 and the isozyme loci linked to it constitute a new linkage group on chromosome 7. The general absence of spacer length classes common to both rRNA loci in any of the lines we examined indicates that little or no genetic exchange occurs between the nonhomologous nucleolar organizer regions.}, number={3}, journal={Theoretical and Applied Genetics}, publisher={Springer Nature America, Inc}, author={Polans, N. O. and Weeden, N. F. and Thompson, W. F.}, year={1986}, month={Jun}, pages={289–295} }
 @article{kaufman_roberts_briggs_thompson_1986, title={Phytochrome Control of Specific mRNA levels in Developing Pea Buds : Kinetics of Accumulation, Reciprocity, and Escape Kinetics of the Low Fluence Response}, volume={81}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.81.4.1033}, DOI={10.1104/pp.81.4.1033}, abstractNote={We have examined the time course for accumulation of each of 12 different nuclear gene transcripts in pea buds after irradiating dark grown seedlings with a single pulse low fluence red light (10(3) micromoles per square meter delivered in 100 seconds). The 12 time courses can be grouped into four general classes. Six transcripts (including RNAs coding for the chlorophyll a/b binding protein and ribulose-1,5-bisphosphate carboxylase) accumulate at a linear rate during 24 hours in darkness following the light pulse. Two transcripts increase rapidly at first but then reach a plateau after 3 hours and remain at that level for the next 21 hours. Another two transcripts exhibit a prolonged lag period before beginning to accumulate, and do not reach significant accumulation rates until 12 to 16 hours after the red light pulse. One transcript appears to undergo a transient increase in abundance in response to red light, but this is superimposed on a background of slowly increasing abundance of this RNA in control plants. This response, unlike all the others, exhibits reciprocity failure in experiments in which the same fluence of light is given over periods ranging between 50 and 4000 seconds.We have also examined the kinetics with which each of these 12 responses escapes from phytochrome-far-red absorbing form control by attempting to reverse the induction with far-red light given at various times after the red light pulse. Again, several different patterns are apparent for the different transcripts. The time at which far red reversibility first begins to be lost, the rate at which it is lost, and the final extent of reversibility remaining after 7 hours in the dark all differ for different transcripts. In addition, we have observed that some responses retain virtually complete photoreversibility for at least 7 hours. In some cases, a comparison of the time course and escape kinetic data indicates that relatively rapid turnover of the RNA must occur. It is not clear whether or not the rate of turnover is influenced by phytochrome.}, number={4}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Kaufman, L. S. and Roberts, L. L. and Briggs, W. R. and Thompson, W. F.}, year={1986}, month={Aug}, pages={1033–1038} }
 @article{watson_thompson_1986, title={Purification and restriction endonuclease analysis of plant nuclear DNA}, volume={118}, DOI={10.1016/0076-6879(86)18064-5}, abstractNote={This chapter discusses the methods for the purification and restriction endonuclease analysis of plant nuclear DNA. The rationale of the methods for the isolation of DNA from purified nuclei have the features, such as a pretreatment of the tissue to enhance cell disruption, homogenization in the presence of membrane stabilizing agents, filtration to remove whole cells and large debris, differential lysis of organelles with Triton X-100 in the presence of divalent cations (Mg 2+ or Ca 2+ ), and purification of the nuclei by density gradient centrifugation. Nuclei are separated from other cellular debris by density centrifugation in suspensions of Percoll, colloidal silica coated with polyvinylpyrolidone. Once the nuclei have been purified, extraction of DNA is accomplished by detergent lysis and thorough protease digestion. Failure to completely digest proteins at this point is the most frequent reason for inability to digest the DNA with restriction enzymes. DNA is separated from RNA and any residual protein by repeated CsCl–ethidium bromide gradient centrifugation.}, journal={Methods in Enzymology}, author={Watson, J.C. and Thompson, W.F.}, year={1986}, pages={57–75} }
 @article{stein_palmer_thompson_1986, title={Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda}, volume={10}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/bf00418530}, DOI={10.1007/bf00418530}, abstractNote={The evolution and recombination of chloroplast genome structure in the fern genus Osmunda were studied by comparative restriction site mapping and filter hybridization of chloroplast DNAs (cpDNAs) from three species — 0. cinnamomea, 0. claytoniana and 0. regalis. The three 144 kb circular genomes were found to be colinear in organization, indicating that no major inversions or transpositions had occurred during the approximately 70 million years since their radiation from a common ancestor. Although overall size and sequence arrangement are highly conserved in the three genomes, they differ by an extensive series of small deletions and insertions, ranging in size from 50 bp to 350 by and scattered more or less at random throughout the circular chromosomes. All three chloroplast genomes contain a large inverted repeat of approximately 10 kb in size. However, hybridizations using cloned fragments from the 0. cinnamomea and 0. regalis genomes revealed the absence of any dispersed repeats in at least 50% of the genome. Analysis with restriction enzymes that fail to cleave the 10 kb inverted repeat indicated that each of the three fern chloroplast genomes exists as an equimolar population of two isomeric circles differing only in the relative orientation of their two single copy regions. These two inversion isomers are inferred to result from high frequency intramolecular recombination between paired inverted repeat segments. In all aspects of their general organization, recombinational heterogeneity, and extent of structural rearrangement and length mutation, these fern chloroplast genomes resemble very closely the chloroplast genomes of most angiosperms.}, number={11}, journal={Current Genetics}, publisher={Springer Nature America, Inc}, author={Stein, Diana B. and Palmer, Jeffrey D. and Thompson, William F.}, year={1986}, month={Jul}, pages={835–841} }
 @article{flavell_o'dell_thompson_vincentz_sardana_barker_1986, title={The differential expression of ribosomal RNA genes}, volume={B314}, DOI={10.1098/rstb.1986.0060}, abstractNote={Ribosomal RNA genes are localized at chromosomal sites termed nucleolus organizers because nucleoli form around transcribed ribosomal RNA genes. The relative activities of arrays of ribosomal RNA genes can be estimated cytologically by comparing the sizes of nucleoli in the same cell. Also, active nucleolus organizers give rise to visible constrictions in metaphase chromosomes whereas inactive nucleolus organizers do not. With these assays the differential expression of nucleolus organizers and ribosomal RNA genes has been observed frequently, especially in interspecies hybrids. Studies on wheat have revealed that differences in gene expression are associated with differences in chromatin structure and cytosine methylation. Active loci have higher proportions of their genes decondensed and accessible to proteins and also higher proportions with a non-methylated cytosine residue at a CCGG site in the region of the promoter. Short, related sequences with dyad symmetry have been noted between —140 and —70 base pairs from where transcription is initiated in a wheat ribosomal RNA gene. Similar sequences are reiterated upstream of the promoter over 2000 base pairs. From comparison of this gene structure with that ofXenopusribosomal RNA genes it can be concluded that these short sequences are likely to act as enhancers of transcription by binding to specific regulatory proteins that function to stimulate the attachment of polymerase I complexes. Differential expression of arrays of ribosomal RNA genes results when genes have different numbers of enhancer repeats or a higher affinity for the regulatory protein(s). This model to explain differential gene expression and the origins of genetic variation affecting ribosomal RNA gene expression are discussed.}, number={1166}, journal={Philosophical Transactions of Royal Society of London}, author={Flavell, R.B. and O'Dell, M. and Thompson, W.F. and Vincentz, M. and Sardana, R. and Barker, R.F.}, year={1986}, pages={385–397} }
 @article{stern_bang_thompson_1986, title={The watermelon mitochondrial URF-1 gene: evidence for a complex structure}, volume={10}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/bf00418532}, DOI={10.1007/bf00418532}, abstractNote={We have cloned and sequenced a fragment of watermelon mitochondrial DNA (mtDNA) which contains a gene homologous to mitochondrial URF-1 (Unidentified Reading Frame-1) of vertebrates, Drosophila yakuba and Aspergillus nidulans. URF-1 is thought to encode a component of the respiratory chain NADH dehydrogenase. Two coding regions in the watermelon gene are separated by approximately 1,450 bp of untranslatable DNA. These two exons encode the central portions of URF-1, and are highly conserved. We postulate that three additional exons, selected by their map location and amino acid homology to other URF-1 sequences, encode the remainder of the polypeptide. This is the first description of a plant mitochondrial gene with multiple introns.}, number={11}, journal={Current Genetics}, publisher={Springer Nature America, Inc}, author={Stern, David B. and Bang, Anne G. and Thompson, William F.}, year={1986}, month={Jul}, pages={857–869} }
 @article{palmer_jorgensen_thompson_1985, title={Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis}, volume={109}, journal={Genetics}, author={Palmer, J.D. and Jorgensen, R.A. and Thompson, W.F.}, year={1985}, pages={195–213} }
 @inbook{flavell_o'dell_smith_thompson_1985, place={New York}, title={Chromosome architecture: the distribution of recombination sites, the structure of ribosomal DNA loci, and the multiplicity of sequences containing inverted repeats}, booktitle={Molecular Form and Function of the Plant Genome}, publisher={Plenum Press}, author={Flavell, R.B. and O'Dell, M. and Smith, D.B. and Thompson, W.F.}, editor={van Vloten-Doting, L. and Groot, G.S.P. and Hall, T.C.Editors}, year={1985} }
 @article{thompson_kaufman_watson_1985, title={Induction of plant gene expression by light}, volume={3}, ISSN={0265-9247 1521-1878}, url={http://dx.doi.org/10.1002/bies.950030405}, DOI={10.1002/bies.950030405}, abstractNote={Abstract}, number={4}, journal={BioEssays}, publisher={Wiley}, author={Thompson, William F. and Kaufman, L. S. and Watson, J. C.}, year={1985}, month={Oct}, pages={153–159} }
 @article{polans_weeden_thompson_1985, title={Inheritance, organization, and mapping of rbcS and cab multigene families in pea}, volume={82}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.82.15.5083}, DOI={10.1073/pnas.82.15.5083}, abstractNote={
            DNA restriction endonuclease fragment patterns corresponding to both the
            rbcS
            and
            cab
            multigene families of pea are each shown to segregate as single Mendelian units in the F
            2
            progeny of two separate crosses. All of the observed variation in each of the multigene families is thus organized on the chromosome in a tightly linked complex. Linkage relationships between both multigene families and an array of morphological and isozyme markers establish the location of the
            rbcS
            and
            cab
            gene clusters on pea chromosomes 5 and 2, respectively. Our results, which indicate a high level of DNA restriction fragment length polymorphism in pea, suggest sufficient variation to permit the construction of a highly detailed linkage map.
          }, number={15}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Polans, N. O. and Weeden, N. F. and Thompson, W. F.}, year={1985}, month={Aug}, pages={5083–5087} }
 @inbook{kaufman_watson_briggs_thompson_1985, title={Photoregulation of nuclear-encoded transcripts: blue light regulation of specific transcript abundance}, DOI={10.1017/S0016672300024733}, abstractNote={tion fragment length polymorphisms) on the different chromosomes. Linkage analysis of familial data using RFLPs is making it possible to locate the chromosome segments carrying particular genes in cases where the molecular pathology of the defect is quite unknown and this is the first essential step in analysis. Recent successes with this approach include Huntingdon's Chorea, Duchenne muscular dystrophy and polycystic disease of the kidney. Oligonucleotide probes have also made it possible to recognise specific gene mutations, e.g. causing sickle cell anaemia, /? thalassaemia and ocl antitrypsin deficiency. Rapid development in this area can be expected, and will certainly lead to a demand for much increased laboratory facilities.}, booktitle={The Molecular Biology of the Photosynthetic Aparatus}, publisher={Cold Spring Harbor Press}, author={Kaufman, L.S. and Watson, J.C. and Briggs, W.R. and Thompson, W.F.}, editor={Steinback, K.E. and Bonitz, S. and Arntzen, C.J. and Bogorad, L.Editors}, year={1985}, pages={367–376} }
 @article{kaufman_briggs_thompson_1985, title={Phytochrome Control of Specific mRNA Levels in Developing Pea Buds : The Presence of Both Very Low Fluence and Low Fluence Responses}, volume={78}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.78.2.388}, DOI={10.1104/pp.78.2.388}, abstractNote={We have examined phytochrome regulated changes in transcript abundance for 11 different light regulated mRNAs in developing pea buds. Fluence-response curves were measured for changes in transcript abundance in response to red light pulses in both the low and very low fluence ranges. Most transcripts show only low fluence responses, with a threshold of approximately 10 micromoles per square meter. All of the low fluence responses are reversible by far red light. One transcript shows a very low fluence response, with a threshold of approximately 10(-4) micromoles per square meter. As expected, the very low fluence response is not far red reversible and in fact can be induced by far red light.Various fluences of red light were also used as pretreatments before transferring seedlings to continuous white light. One transcript responds to pretreatments in the very low fluence range, several respond to pretreatments in the low fluence range (including chlorophyll a/b binding protein RNA and ribulose-1,5-bisphosphate carboxylase RNA), and several show no response to the red light under these conditions. The threshold of these low fluence responses is approximately 10(2) micromoles per square meter, one order of magnitude greater than the threshold of the low fluence responses to red light alone.The transcripts may also be grouped by their responses to white light treatment alone. Three of the clones correspond to transcripts whose abundance decreases after a 24 hour white light treatment. The remainder of the mRNAs increase between 2- and 10-fold in response to the 24 hour white light.}, number={2}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Kaufman, L. S. and Briggs, W. R. and Thompson, W. F.}, year={1985}, month={Jun}, pages={388–393} }
 @inbook{briggs_mandoli_shinkle_kaufman_watson_thompson_1985, title={Phytochrome Regulation of Plant Development at the Whole Plant, Physiological, and Molecular Levels}, ISBN={9781461295112 9781461324973}, url={http://dx.doi.org/10.1007/978-1-4613-2497-3_16}, DOI={10.1007/978-1-4613-2497-3_16}, booktitle={Sensory Perception and Transduction in Aneural Organisms}, publisher={Springer US}, author={Briggs, Winslow R. and Mandoli, Dina F. and Shinkle, James R. and Kaufman, Lon S. and Watson, John C. and Thompson, William F.}, year={1985}, pages={265–280} }
 @article{kaufman_thompson_briggs_1984, title={Different red light requirements for phytochrome-induced accumulation of Cab RNA and RbcS RNA}, volume={226}, DOI={10.1126/science.226.4681.1447}, abstractNote={
            For several species of plants the abundance of those transcripts encoding the chlorophyll a/b binding protein (
            cab
            RNA) and the small subunit of ribulose-1,5-biphosphate carboxylase-oxygenase (
            rbcS
            RNA) has been established as being under the control of phytochrome. However, this conclusion does not take into account the various types of phytochrome control based on both the fluence of red light necessary to induce the response and the ability of far red light either to induce or to reverse the response. The fluence of red light necessary to induce the accumulation of
            rbcS
            RNA was found to be 10,000 times greater than that necessary to induce the accumulation of
            cab
            RNA. Furthermore, far red light alone was capable of inducing the accumulation of
            cab
            RNA. It is possible, therefore, that developing pea buds accumulate
            cab
            RNA before
            rbcS
            and that
            cab
            RNA is not subject to the normal end-of-day signals affecting many phytochrome responses.
          }, number={4681}, journal={Science}, author={Kaufman, L.S. and Thompson, W.F. and Briggs, W.R.}, year={1984}, month={Dec}, pages={1447–1449} }
 @inbook{palmer_osorio_watson_edwards_dodd_thompson_1984, place={New York}, title={Evolutionary aspects of chloroplast genome expression and organization}, volume={14}, booktitle={Biosynthesis of the Photosynthetic Apparatus: Molecular Biology, Development and Regulation}, publisher={UCLA Symposia on Molecular and Cellular Biology, New Series}, author={Palmer, J.D. and Osorio, B. and Watson, J.C. and Edwards, H. and Dodd, J. and Thompson, W.F.}, editor={Hallick, R. and Staehelin, L.A. and Thornber, J.P. and Liss, Alan R.Editors}, year={1984}, pages={273–283} }
 @inbook{watson_palmer_thompson_1983, title={Chloroplast genes for components of the translational apparatus}, volume={82}, booktitle={Carnegie Institution Washington Year Book}, author={Watson, J.C. and Palmer, J.D. and Thompson, W.F.}, year={1983}, pages={24–26} }
 @inproceedings{flavell_o'dell_thompson_1983, title={Cytosine methylation of ribosomal RNA genes and nucleolus organizer activity in wheat}, booktitle={Proceedings of the Kew Chromosome Conference II}, author={Flavell, R.B. and O'Dell, M. and Thompson, W.F.}, year={1983}, pages={11–17} }
 @article{spiker_murray_thompson_1983, title={DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants.}, volume={80}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.80.3.815}, DOI={10.1073/pnas.80.3.815}, abstractNote={We have investigated the DNase I sensitivity of transcriptionally active DNA sequences in intact nuclei and isolated chromatin from embryos of wheat (Triticum aestivum L.). Nuclei or isolated chromatin was incubated with DNase I, and the extent of DNA digestion was monitored as percentage acid solubility. The resistant DNA and DNA from sham-digested controls were used to drive reassociation reactions with cDNA populations corresponding to either total poly(A)+RNA from unimbibed wheat embryos or polysomal poly(A)+RNA from embryos that had imbibed for 3 hr. Sequences complementary to either probe were depleted in DNase I-resistant DNA from nuclei and from chromatin isolated under low-ionic-strength conditions. This indicates that transcriptionally active sequences are preferentially DNase I sensitive in plants. In chromatin isolated at higher ionic strength, cDNA complementary sequences were not preferentially depleted by DNase I treatment. Therefore, the chromatin structure that confers preferential DNase I sensitivity to transcriptionally active genes appears to be lost when the higher-ionic-strength method of preparation is used. Treatment of wheat nuclei with DNase I causes the release of four prominent nonhistone chromosomal proteins that comigrate with wheat high mobility group proteins on NaDodSO4 gels.}, number={3}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Spiker, S. and Murray, M. G. and Thompson, W. F.}, year={1983}, month={Feb}, pages={815–819} }
 @article{stern_palmer_thompson_lonsdale_1983, title={Mitochondrial DNA sequence evolution and homology to chloroplast DNA in angiosperms}, volume={12}, journal={UCLA Symposia on Molecular and Cellular Biology}, author={Stern, D.B. and Palmer, J.D. and Thompson, W.F. and Lonsdale, D.M.}, year={1983}, pages={467–477} }
 @article{thompson_everett_polans_jorgensen_palmer_1983, title={Phytochrome control of RNA levels in developing pea and mung-bean leaves}, volume={158}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/bf00397240}, DOI={10.1007/bf00397240}, abstractNote={We have examined phytochrome effects on the abundance of transcripts from several nuclear and chloroplast genes in buds of dark-grown pea seedlings and primary leaves of dark-grown mung-bean seedlings. Probes for nuclear-coded RNAs were selected from a library of cDNA clones and included those corresponding to the small subunit (SS) of ribulosebisphosphate carboxylase and a chlorophyll a/b binding protein (AB). Transcripts from chloroplast genes for RuBP carboxylase large subunit (LS) and a 32,000-dalton photosystem II polypeptide (PII) were assayed with cloned fragments of the chloroplast genome. In addition, we present data on transcripts from a number of other nuclear genes of unknown function, several of which change in abundance during light-induced development. Transcript levels were measured as a proportion of total RNA by a dot blot assay in which RNA from different tissues or stages is fixed to nitrocellulose and hybridized with (32)P-labeled probes prepared from cloned DNAs. Several patterns of induction can be seen. For example, although both SS and AB RNAs show positive, red/far-red reversible responses in both pea and mung bean, in pea buds the induction ratio for SS RNA is much higher than that for AB RNA, while just the reverse is true for mung-bean leaves. In addition, treatment with lowfluence red light produces full induction of the pea AB RNA, while SS RNA in the same tissue does not reach a maximum steady-state level until after about 24 h of supplementary high-intensity white light. In pea buds, chloroplast genes (LS, PII) also show clear responses to phytochrome, as measured by the steady-state levels of their RNA products. Chloroplast DNA levels (as a fraction of the total cellular DNA) show the same response pattern, which may indicate that in peas many of the light effects we see are related to a general stimulation of chloroplast development. In mung beans, the levels of plastid DNA and RNA are already quite high in the leaves of 7-d dark-grown seedlings, and light effects are much less pronounced. The results are consistent with the notion that chloroplast development is arrested at a later stage in dark-grown mung-bean leaves than in etiolated pea buds.}, number={6}, journal={Planta}, publisher={Springer Nature America, Inc}, author={Thompson, William F. and Everett, Marylee and Polans, Neil O. and Jorgensen, Richard A. and Palmer, Jeffrey D.}, year={1983}, month={Aug}, pages={487–500} }
 @article{palmer_thompson_1982, title={Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost}, volume={29}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/0092-8674(82)90170-2}, DOI={10.1016/0092-8674(82)90170-2}, abstractNote={We examined the arrangement of sequences common to seven angiosperm chloroplast genomes. The chloroplast DNAs of spinach, petunia and cucumber are essentially colinear. They share with the corn chloroplast genome a large inversion of ∼50 kb relative to the genomes of three legumes—mung bean, pea and broad bean. There is one additional rearrangement, a second, smaller inversion within the 50 kb inversion, which is specific to the corn genome. These two changes are the only detectable rearrangements that have occurred during the evolution of the species examined (corn, spinach, petunia, cucumber and mung bean) whose chloroplast genomes contain a large inverted repeat sequence of 22–25 kb. In contrast, we find extensive sequence rearrangements in comparing the pea and broad bean genomes, both of which have deleted one entire segment of the inverted repeat, and also in comparing each of these to the mung bean genome. Thus there is a relatively stable arrangement of sequences in those genomes with the inverted repeat and a much more dynamic arrangement in those that have lost it. We discuss several explanations for this correlation, including the possibility that the inverted repeat may play a direct role in maintaining a conserved arrangement of chloroplast DNA sequences.}, number={2}, journal={Cell}, publisher={Elsevier BV}, author={Palmer, Jeffrey D. and Thompson, William F.}, year={1982}, month={Jun}, pages={537–550} }
 @inbook{jorgensen_cuellar_thompson_1982, title={Modes and tempos in the evolution of nuclear-encoded ribosomal RNA genes in legumes}, volume={81}, booktitle={Carnegie Institution of Washington Year Book}, author={Jorgensen, R.A. and Cuellar, R.E. and Thompson, W.F.}, year={1982}, pages={98–101} }
 @article{palmer_edwards_jorgensen_thompson_1982, title={Novel evolutionary variation in transcription and location of two chloroplast genes}, volume={10}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/10.21.6819}, DOI={10.1093/nar/10.21.6819}, abstractNote={We have found major evolutionary changes in the types of transcripts produced by specific chloroplast genes, in particular those encoding the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase and a photosystem II polypeptide (PII). Two distinct patterns of LS gene transcripts are revealed by hybridizing an LS gene probe to electrophoretically separated RNA from 19 angiosperms. Most species, including pea, contain the single transcript of approximately 1.6 kb previously observed in corn, spinach and mustard. However, in mung bean and other members of the legume genera Vigna and Phaseolus, the 1.6 kb transcript represents only a minor fraction of LS transcripts, and instead, two larger LS transcripts of approximately 2.4 and 2.6 kb predominate. The PII gene produces a single transcript in pea and most other species examined, while members of the related legume genera Vigna, Phaseolus and Glycine contain two additional transcripts which are smaller in size and probably represent specific RNA breakdown products. A single species, sweet pea (Lathyrus odoratus), contains a second PII transcript which is 0.2 kb larger than the approximately 1.2 kb transcript found in all species. The LS and PII genes map to the same 5 kb region in both pea and mung bean and are transcribed off the same DNA strand. In contrast, published studies indicate that the two genes are approximately 50 kb apart and are transcribed off opposite DNA strands in five other chloroplast genomes. These differences are probably the consequence of an approximately 50 kb inversion which distinguishes the pea and mung bean genomes from those of most other angiosperms (1).}, number={21}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Palmer, Jeffrey D. and Edwards, Helen and Jorgensen, Richard A. and Thompson, William F.}, year={1982}, pages={6819–6832} }
 @article{murray_thompson_1982, title={Repeat sequence interspersion in coding DNA of peas does not reflect that in total pea DNA}, volume={1}, DOI={10.1007/bf00024977}, abstractNote={The pattern of sequence organization in the regions of the pea genome near sequences coding for mRNA differs significantly from that in total DNA. Interspersion of repeated and single copy sequences is so extensive that 85% of 1300 nucleotide-long fragments contain highly repetitive sequences (about 5000 copies per haploid genome). However, data presented here demonstrate that sequences which code for mRNA are enriched in the small fraction of fragments which do not contain these highly repetitive sequences. Thus, in contrast to the great majority of other sequences in the genome, most mRNA coding sequences are not located within 1300 nucleotides of highly repetitive elements. Moreover, our data indicate that those repeats (if any) which are closely associated with mRNA coding sequences belong to low copy number families characterized by an unusually low degree of sequence divergence.}, number={2}, journal={Plant Molecular Biology}, author={Murray, M.G. and Thompson, W.F.}, year={1982}, pages={143–153} }
 @article{murray_peters_thompson_1981, title={Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution}, volume={17}, ISSN={0022-2844 1432-1432}, url={http://dx.doi.org/10.1007/bf01792422}, DOI={10.1007/bf01792422}, number={1}, journal={Journal of Molecular Evolution}, publisher={Springer Nature}, author={Murray, Michael G. and Peters, Debra L. and Thompson, William F.}, year={1981}, month={Jan}, pages={31–42} }
 @article{palmer_thompson_1981, title={Clone banks of the mung bean, pea and spinach chloroplast genomes}, volume={15}, ISSN={0378-1119}, url={http://dx.doi.org/10.1016/0378-1119(81)90100-1}, DOI={10.1016/0378-1119(81)90100-1}, abstractNote={All but one of the PstI restriction fragments from mung bean, pea, and spinach chloroplast DNAs have been stably cloned into pBR322. Large fragments (15–54 kb) were cloned at low efficiencies which decreased with increasing fragment length. However, plasmids containing fragments above 25–30 kb were too unstable to be useful. In particular, pBR322 derivatives containing the largest mung bean and spinach fragments (34 kb and 54 kb, respectively) are extremely unstable and rapidly delete parts of the plasmid sequence. The SalI fragments of mung bean chloroplast DNA which cover the 34-kb PstI fragment have been cloned into pBR322. Similarly, the XhoI fragments of spinach chloroplast DNA which cover all but 0.9 kb of the 54-kb PstI fragment have been cloned into pACYC177. After a search of several thousand recombinants we were unable to recover a clone containing a 12.2-kb pea chloroplast PstI fragment and suggest that some property of its sequence may be inimical to the cloning process. The identity of the cloned fragments to native chloroplast DNA restriction fragments is demonstrated by restriction analysis and by the ability to construct detailed restriction maps of the mung bean and pea chloroplast genomes.}, number={1}, journal={Gene}, publisher={Elsevier BV}, author={Palmer, Jeffrey D. and Thompson, William F.}, year={1981}, month={Oct}, pages={21–26} }
 @inbook{cuellar_thompson_1981, title={Complex organization of repetitive DNA families as analyzed with cloned DNA fragments}, volume={80}, booktitle={Carnegie Institution of Washington Year Book}, author={Cuellar, R.E. and Thompson, W.F.}, year={1981}, pages={81–82} }
 @inbook{belford_thompson_stein_1981, place={ NY}, title={DNA hybridization techniques for the study of plant evolution}, booktitle={Phytochemistry and Angiosperm Phylogeny}, publisher={Praeger Scientific}, author={Belford, H.S. and Thompson, W.F. and Stein, D.B.}, editor={Young, D.A. and Seigler, D.S.Editors}, year={1981}, pages={1–18} }
 @article{preisler_thompson_1981, title={Evolutionary sequence divergence within repeated DNA families of higher plant genomes}, volume={17}, ISSN={0022-2844 1432-1432}, url={http://dx.doi.org/10.1007/bf01732678}, DOI={10.1007/bf01732678}, abstractNote={An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was confirmed by the use of deaminated Escherichia coli DNA models for repetitive families. The melting data for DNA reassociated at two different temperatures provided strong evidence that Pisum sativum repeated families are mostly heterogeneous, while homogeneous families predominate in Vigna radiata. These findings, together with other differences between the two genomes, suggest that the rate of sequence amplification has been higher in the evolutionary history of Pisum DNA. A general trend seems to exist for high amplification rates in large, highly repetitive plant genomes such as Pisum and lower rates in smaller plant genomes such as Vigna, as well as in the generally smaller, less repetitive genomes of most animal species.}, number={2}, journal={Journal of Molecular Evolution}, publisher={Springer Nature}, author={Preisler, Richard S. and Thompson, William F.}, year={1981}, month={Mar}, pages={85–93} }
 @article{preisler_thompson_1981, title={Evolutionary sequence divergence within repeated DNA families of higher plant genomes}, volume={17}, ISSN={0022-2844 1432-1432}, url={http://dx.doi.org/10.1007/bf01732677}, DOI={10.1007/bf01732677}, abstractNote={The higher proportion of repeated DNA sequences in the garden pea (Pisum sativum) than in the mung bean (Vigna radiata), as well as other differences between these legume genomes, are consistent with a higher rate of sequence amplification in the former. This hypothesis leads to a prediction that repeated sequence families in Pisum are mostly heterogeneous, as defined by Bendich and Anderson (1977), while Vigna families are homogeneous. An assay developed by these authors to distinguish between the two types of families, by comparison of reassociation rates at different temperatures, was utilized. The results for Vigna defied the predictions of the assay for either homogeneous or heterogeneous model. Evaluation of the kinetic data in light of the great diversity of repeated family copy numbers in both genomes enabled an interpretation of the results as consistent with heterogeneous families in Pisum and homogeneous families in Vigna. These tentative conclusions were supported by the results of a thermal denaturation (melting) assay described in the accompanying paper.}, number={2}, journal={Journal of Molecular Evolution}, publisher={Springer Nature}, author={Preisler, Richard S. and Thompson, William F.}, year={1981}, month={Mar}, pages={78–84} }
 @article{palmer_thompson_1981, title={Rearrangements in the chloroplast genomes of mung bean and pea}, volume={78}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.78.9.5533}, DOI={10.1073/pnas.78.9.5533}, abstractNote={
            We have mapped all the cleavage sites for the restriction endonucleases
            Bst
            EII,
            Kpn
            I,
            Pst
            I,
            Pvu
            II,
            Sac
            I,
            Sal
            I,
            Sma
            I, and
            Xho
            I on the circular chloroplast chromosomes from mung bean and pea. The mung bean chloroplast genome measures 150 kilobase pairs (kb) in length; it includes two identical sequences of 23 kb that contain the ribosomal genes and are arranged as an inverted repeat separated by single-copy regions of 21 and 83 kb. The pea chloroplast genome is only 120 kb in size, has only one set of ribosomal genes, and does not possess any detectable repeated sequences. The mung bean inverted repeat structure is common to all other nonleguminous higher plant chloroplast genomes studied, whereas the pea structure has been found only in the closely related legume
            Vicia faba
            . We conclude from these data that loss of one copy of the inverted repeat sequence has occurred only rarely during the evolution of the Angiosperms, and in the case of the legumes after the divergence of the mung bean line from the pea-
            Vicia
            line. We present hybridization data indicating that rearrangements that change the linear order of homologous sequences within the chloroplast genome have been quite frequent during the course of legume evolution.
          }, number={9}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Palmer, J. D. and Thompson, W. F.}, year={1981}, month={Sep}, pages={5533–5537} }
 @article{belford_thompson_1981, title={Single copy DNA homologies in Atriplex. I. Cross reactivity estimates and the role of deletions in genome evolution}, volume={46}, ISSN={0018-067X 1365-2540}, url={http://dx.doi.org/10.1038/hdy.1981.9}, DOI={10.1038/hdy.1981.9}, abstractNote={Genome sizes and single copy complexity values have been estimated for eight Atriplex species and spinach by analysis of DNA reassociation kinetics. These values, together with measurements of interspecific hybridization carried out with purified single copy tracers, have been used to estimate the absolute amount of single copy DNA which is composed of homologous sequences in various species. The data show a large variation in cross reactivity for different species pairs which is best explained by postulating that these genomes were subject to extensive deletion during evolution of different lineages. At most, only about 5 × 107 nucleotide pairs of single copy DNA (about 10 times the amount in an E. coli genome) appear to be necessary to specify phenotypic features common to Atriplex species.}, number={1}, journal={Heredity}, publisher={Springer Nature}, author={Belford, Heather S and Thompson, William F}, year={1981}, month={Feb}, pages={91–108} }
 @article{belford_thompson_1981, title={Single copy DNA homologies in Atriplex. II. Hybrid thermal stabilities and molecular phylogeny}, volume={46}, DOI={10.1038/hdy.1981.10}, abstractNote={Single copy DNA sequence homologies were measured by interspecific molecular hybridization and thermal denaturation techniques for eight species of the genus Atriplex and spinach (Spinacia oleracea). Thermal stability profiles for Atriplex interspecific hybrids indicated more base pair mismatch than has been observed in most previously reported intrageneric comparisons of animal DNA. On the assumption that sequence divergence by base substitution is proportional to the time which has elapsed subsequent to speciation, the data are interpreted as indicating that lines leading to many modern Atriplex species probably originated during a single period of rapid speciation. This group includes C3 and C4 photosynthetic types from both subgenera. Thus the molecular data do not support the classical subgeneric distinction, and it is no longer necessary to postulate a polyphyletic origin for C4 photosynthesis within Atriplex.}, number={1}, journal={Heredity}, author={Belford, H.S. and Thompson, W.F.}, year={1981}, month={Feb}, pages={109–122} }
 @inbook{thompson_murray_1981, title={The nuclear genome: Structure and Function}, volume={6}, booktitle={The Biochemistry of Plants}, author={Thompson, W.F. and Murray, M.G.}, editor={Marcus, A.Editor}, year={1981}, pages={1–81} }
 @inbook{thompson_murray_cuellar_1980, title={Contrasting Patterns of DNA Sequence Organization in Plants}, ISBN={9781461330530 9781461330516}, url={http://dx.doi.org/10.1007/978-1-4613-3051-6_1}, DOI={10.1007/978-1-4613-3051-6_1}, booktitle={Genome Organization and Expression in Plants}, publisher={Springer US}, author={Thompson, W. F. and Murray, M. G. and Cuellar, R. E.}, year={1980}, pages={1–15} }
 @inbook{thompson_murray_belford_cuellar_1980, title={Patterns of DNA sequence repetition and interspersion in higher plants}, booktitle={Genetic Improvement of Crops}, publisher={University of Minnesota Press}, author={Thompson, W.F. and Murray, M.G. and Belford, H.S. and Cuellar, R.E.}, editor={Rubenstein, I. and Phillips, R.L. and Green, C.E. and Gegenbach, B.G.Editors}, year={1980}, pages={47–75} }
 @article{murray_thompson_1980, title={Rapid isolation of high molecular weight plant DNA}, volume={8}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/8.19.4321}, DOI={10.1093/nar/8.19.4321}, abstractNote={A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.}, number={19}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Murray, M.G. and Thompson, W.F.}, year={1980}, pages={4321–4326} }
 @inbook{thompson_murray_1980, place={Norwich, England}, title={Sequence organization in pea and mung bean DNA and a model for genome evolution}, booktitle={The Plant Genome}, publisher={John Innes Charity}, author={Thompson, W.F. and Murray, M.G.}, editor={Davies, D.R. and Hopwood, D.A.Editors}, year={1980}, pages={31–45} }
 @inbook{palmer_thompson_1980, title={Studies on higher plant chloroplast and mitochondrial DNA}, volume={79}, booktitle={Carnegie Institution of Washington Year Book}, author={Palmer, J.D. and Thompson, W.F.}, year={1980}, pages={120–123} }
 @inbook{cuellar_selker_thompson_1979, title={Cloning of plant DNA. Comparison of five host strains of Escherichia coli}, volume={78}, booktitle={Carnegie Institution of Washington Year Book}, author={Cuellar, R.E. and Selker, E.U. and Thompson, W.F.}, year={1979}, pages={215–217} }
 @article{murray_palmer_cuellar_thompson_1979, title={DNA sequence organization in the mung bean genome}, volume={18}, DOI={10.1021/bi00590a034}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVArticleDeoxyribonucleic acid sequence organization in the mung bean genomeMichael G. Murray, Jeffrey D. Palmer, Richard E. Cuellar, and William F. ThompsonCite this: Biochemistry 1979, 18, 23, 5259–5266Publication Date (Print):November 13, 1979Publication History Published online1 May 2002Published inissue 13 November 1979https://doi.org/10.1021/bi00590a034RIGHTS & PERMISSIONSArticle Views54Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (960 KB) Get e-Alerts Get e-Alerts}, number={23}, journal={Biochemistry}, author={Murray, M.G. and Palmer, J.D. and Cuellar, R.E. and Thompson, W.F.}, year={1979}, pages={5259–5266} }
 @article{stein_thompson_belford_1979, title={Studies on DNA sequence in the Osmundaceae}, volume={13}, DOI={10.1007/bf01739481}, abstractNote={Phylogenetic relationships of Osmunda cinnamomea, O. claytoniana, and O. regalis were explored by means of DNA sequence comparisons. Hydroxyapatite thermal elution profiles of self-reassociated repetitive DNA fragments were very similar, indicating the absence of gross differences in the amount of recent amplification or addition of repetitive DNA in any of these three genomes. Interspecific DNA sequence comparisons showed, in contrast to our earlier interpretation, that repeated DNA sequences of O. claytoniana are nearly equally diverged from those of O. cinnamomea and O. regalis. Differences between repetitive sequences of the three species can be interpreted as reflecting amplification events which occurred subsequent to speciation. The data obtained suggest that the three Osmunda species most likely arose more or less simultaneously from a common ancestor. These findings were verified in experiments with tracer DNA preparations enriched for single copy sequences. On the basis of the hydridization data presented here and of the fossil record, the rate of single copy sequence divergence in the ferns is comparable to that in the primates, although slower than that observed in other animal taxa. From this first evaluation of rates of DNA evolution in plants it would seem that the rates for plants and animals are roughly comparable. The evidence suggests that species divergence is accompanied by further reiteration of preexisting repeat sequences. The rate of addition of repetitive sequences probably is slower in ferns than in angiosperms. This difference might be attributable to the much larger effective generation time in ferns.}, number={3}, journal={Journal of Molecular Evolution}, author={Stein, D.B. and Thompson, W.F. and Belford, H.S.}, year={1979}, month={Sep}, pages={215–232} }
 @inbook{palmer_murray_thompson_1979, title={Studies on chloroplast DNA of mung bean and pea}, volume={78}, booktitle={Carnegie Institution of Washington Year Book}, author={Palmer, J.D. and Murray, M.G. and Thompson, W.F.}, year={1979}, pages={226–231} }
 @article{cuellar_ford_briggs_thompson_1978, title={Application of higher derivative techniques to analysis of high-resolution thermal denaturation profiles of reassociated repetitive DNA.}, volume={75}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.75.12.6026}, DOI={10.1073/pnas.75.12.6026}, abstractNote={We have analyzed high-resolution denaturation profiles of reassociated repetitive DNA sequences by using a combination of higher derivative analysis and curve-fitting techniques. Procedures originally used for resolution of components in complex absorption spectra were found to be applicable to high-resolution analysis of melting profiles of reassociated repetitive DNA sequences from pea DNA. Under conditions that eliminate the base composition effect on thermal stability (2.4 M tetraethylammonium chloride), such an anlysis can distinquish "thermal classes" of repetitive DNA duplexes exhibiting different amounts of base pair mismatch. Only a single thermal class is observed in reassociated Escherichia coli DNA whereas at least five classes can be reproducibly distinguished in pea and mung bean DNAs.}, number={12}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Cuellar, R. E. and Ford, G. A. and Briggs, W. R. and Thompson, W. F.}, year={1978}, month={Dec}, pages={6026–6030} }
 @article{murray_cuellar_thompson_1978, title={DNA sequence organization in the pea genome}, volume={17}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi00619a027}, DOI={10.1021/bi00619a027}, abstractNote={The reassociation kinetics of pea (Pisum sativum L.) DNA fragments (300 nucleotides) were measured with hydroxylapatite. The most slowly reassociating fragments do so with a rate constant of 2 X 10(-4) L mol-1s-1, as determined from experiments with total DNA as well as with a tracer enriched for slowly renaturing sequences. This rate is about 1000 times slower than that observed for Escherichia coli DNA included as an internal kinetic standard, indicating a kinetic complexity of 4.5 X 10(9) nucleotide pairs or 4.6 pg of DNA per haploid nucleus. This estimate is in good agreement with previous chemical and cytophotometric measurements. The majority (85%) of the 300 nucleotide fragments contain repetitive sequences. While the reassociation of repetitive DNA could be modeled with two theoretical second-order components, the data did not specify a unique solution. The reassociation kinetics of isolated high- and low-frequency fractions indicate that repetitive sequence families in pea DNA probably cover a broad range of frequencies ranging from 100 to 10 000 or more copies per haploid genome. Single-copy sequences account for about 30% of the DNA, but because of extensive interpersion of repetitive sequences only about 15% of 300 nucleotide fragments reassociate with single-copy kinetics. From studies of hydroxylapatite binding as a function of fragment length, we conclude that the major class of single-copy sequences has a modal length of about 300 nucleotides. Long tracer reassociation kinetics indicate that sequences with an apparent repetition frequency of about 10 000 copies are interspersed at intervals of less than 1300 nucleotides throughout 75% of the genome. At a detection limit of about 3%, we find no single-copy sequences longer than 1000 nucleotides.}, number={26}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Murray, Michael G. and Cuellar, Richard E. and Thompson, William F.}, year={1978}, month={Dec}, pages={5781–5790} }
 @inbook{thompson_1978, title={Perspectives on the evolution of plant DNA}, volume={77}, booktitle={Carnegie Institution of Washington Year Book}, author={Thompson, W.F.}, year={1978}, pages={310–316} }
 @inbook{murray_belford_thompson_1977, title={Contaminants affecting plant DNA reassociation}, volume={76}, booktitle={Carnegie Institution of Washington Year Book}, author={Murray, M.G. and Belford, H.S. and Thompson, W.F.}, year={1977}, pages={255–259} }
 @inbook{murray_belford_thompson_1977, title={In vitro labeling of single stranded DNA}, volume={76}, booktitle={Carnegie Institution of Washington Year Book}, author={Murray, M.G. and Belford, H.S. and Thompson, W.F.}, year={1977}, pages={262–267} }
 @inbook{stein_thompson_1977, title={Interspecific hybridization of fern DNA}, volume={76}, booktitle={Carnegie Institution of Washington Year Book}, author={Stein, D.B. and Thompson, W.F.}, year={1977}, pages={252–255} }
 @article{stein_thompson_1977, title={Isolation of DNA from tannin-containing plants}, volume={11}, DOI={10.1016/0304-4211(78)90018-4}, abstractNote={Abstract A combination of techniques has been developed which permits purification of large amounts of DNA from plants containing high levels of tannins and brown pigments. The method uses lyophilized plant tissue, permitting storage of field collections and eliminating the need for fresh material. The tissue is disrupted by blending at 60° C. The DNA is separated by gel fractionation followed by hydroxyapatite (HAP) chromatography and the final product is concentrated by lyophilization. In this procedure all enzyme treatments and precipitation steps may be avoided.}, number={3-4}, journal={Plant Science Letters}, author={Stein, D.B. and Thompson, W.F.}, year={1977}, pages={323–328} }
 @inbook{rogler_cohen_thompson_1977, title={Restriction endonuclease analysis of Agrobacterium plasmids}, volume={76}, booktitle={Carnegie Institution of Washington Year Book}, author={Rogler, C.E. and Cohen, S.N. and Thompson, W.F.}, year={1977}, pages={267–273} }
 @inbook{murray_thompson_1977, title={Single-strand DNA fragment length determination by alkaline agarose electrophoresis: Applications for DNA renaturation studies}, volume={76}, booktitle={Carnegie Institution of Washington Year Book}, author={Murray, M.G. and Thompson, W.F.}, year={1977}, pages={259–262} }
 @article{thompson_1976, title={Aggregate Formation from Short Fragments of Plant DNA}, volume={57}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.57.4.617}, DOI={10.1104/pp.57.4.617}, abstractNote={Large aggregates have been observed after partial reassociation of pea (Pisum sativum L.) DNA preparations sheared to mean single strand fragment lengths as short as 350 nucleotides. At high DNA concentrations and conditions of salt and temperature which require only moderate precision of base pairing, aggregates pelletable by brief centrifugation account for 30 to 40% of the total DNA from peas, while calf thymus DNA reassociated under similar conditions forms less than 10% pelletable structures. In contrast to networks formed during the reassociation of long DNA fragments containing interspersed repetitive sequences, these aggregates contain a high percentage of double-stranded DNA and are enriched in repetitive sequences.Aggregates detectable by centrifugation do not begin to appear until after extensive repetitive sequence reassociation has already occurred. The results are consistent with a model involving secondary reassociation between single-stranded regions ("hanging tails") remaining after initial duplex formation. This process would lead to formation of large multimers of the original fragments, analogous to the large hyperpolymers which have been observed in extensively reassociated prokaryotic DNA. Randomly sheared fragments containing short (about 300 base pairs) repetitive sequences interspersed with single copy DNA would not be expected to hyperpolymerize significantly under these conditions. I suggest, as a working hypothesis, that much of the repetitive sequence DNA in peas is contained in regions considerably longer than 300 base pairs.}, number={4}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Thompson, W. F.}, year={1976}, month={Apr}, pages={617–622} }
 @inbook{rogler_thompson_1976, title={Plasmid modification associated with loss and acquisition of virulence in Agrobacterium tumefaciens}, volume={75}, booktitle={Carnegie Institution of Washington Year Book}, author={Rogler, C.E. and Thompson, W.F.}, year={1976}, pages={367–373} }
 @article{stein_thompson_1975, title={DNA Hybridization and Evolutionary Relationships in Three Osmunda Species}, volume={189}, ISSN={0036-8075 1095-9203}, url={http://dx.doi.org/10.1126/science.189.4206.888}, DOI={10.1126/science.189.4206.888}, abstractNote={
            Molecular hybridization techniques have been used to estimate the degree of DNA base sequence homology between some members of the fern genus
            Osmunda
            . Under conditions permitting extensive reassociation, measurements of the extent of interspecific reaction and the thermal stability of the hybrid molecules indicated that
            O. claytoniana
            L. (interrupted fern) shares more DNA homology with
            O. cinnamomea
            L. (cinnamon fern) than it does with
            O. regalis
            L. (royal fern). These findings are in conflict with predictions from a recent analysis of living and fossil specimens by numerical techniques. However, they are consistent with the earlier, more traditional, taxonomic assignments.
          }, number={4206}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Stein, D. B. and Thompson, W. F.}, year={1975}, month={Sep}, pages={888–890} }
 @article{gardner_thompson_briggs_1974, title={Differential reactivity of the red-and far-red-absorbing forms of phytochrome to [14C] N-ethyl maleimide}, volume={117}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/bf00388032}, DOI={10.1007/bf00388032}, abstractNote={The red-absorbing form (P r ) and the far-red absorbing form (P fr ) of undergraded, high-molecular-weight phytochrome from rye (Secale cereale L.) seedlings were examined for their reactivity toward N-ethyl-[(14)C]maleimide ([(14)C]-NEM). After pre-treatment of P r with cold NEM and extensive dialysis, photoconversion to P fr and treatment with [(14)C]NEM resulted in an approximately 70% increase in incorporation of radioactivity over the dark control. These results are discussed in relation to the view that phytochrome undergoes a protein conformational change upon phototransformation.}, number={4}, journal={Planta}, publisher={Springer Nature America, Inc}, author={Gardner, Gary and Thompson, William F. and Briggs, Winslow R.}, year={1974}, pages={367–372} }
 @article{thompson_cleland_1972, title={Effect of light and gibberellin on RNA synthesis in pea stem tissue as studied by DNA/RNA hybridization}, volume={50}, DOI={10.1104/pp.50.2.289}, abstractNote={The ability of gibberellin and light to alter gene transcription in dwarf pea (Pisum sativum L., var. Progress No. 9) stem issues has been investigated by means of DNA/RNA hybridization-competition techniques. Distinct changes in hybridizable RNA are caused by a 24-hour pretreatment of the seedlings with light, but no changes in RNA were detected up to 50 hours after treatment of the seedlings with gibberellin. Gibberellin is similar to auxin in its ability to induce stem growth without causing detectable changes in hybridizable RNA.}, journal={Plant Physiology}, author={Thompson, W.F. and Cleland, R.}, year={1972}, pages={289–292} }
 @article{thompson_cleland_1971, title={Auxin and Ribonucleic Acid Synthesis in Pea Stem Tissue as Studied by Deoxyribonucleic Acid-Ribonucleic Acid Hybridization}, volume={48}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.48.6.663}, DOI={10.1104/pp.48.6.663}, abstractNote={The ability of auxin to alter gene transcription in pea (Pisum sativum L.) stem tissues has been investigated by means of DNA/RNA hybridization-competition techniques. In order to obtain reproducible hybridization with total nucleic acid preparations from plants it was found necessary to remove interfering substances, probably polysaccharides; this was accomplished by methoxyethanol extraction and precipitation with cetyltrimethylammonium bromide. When purified in this fashion, plant nucleic acids could be made to form hybrids which showed both species specificity and high thermal stability.No change in hybridizable RNA of stem sections in response to auxin could be detected over a 2- to 24-hour period, regardless of the auxin level employed. In contrast, when large doses of auxin were applied to intact pea seedlings, definite changes in the hybridizable RNA of stem tissue were detected both 8 and 24 hours after treatment. Many of the 2,4-D-induced species of RNA which were present at 24 hours were also present at 8 hours. Sections apparently lack a factor needed for the manifestation of the auxin effect on RNA synthesis.Since the hybridization assay employed does not measure all cellular RNA, it is still possible that certain RNA species may be synthesized in sections in response to auxin. However, the auxin promotion of cell elongation in such sections is clearly not associated with changes in hybridizable RNA such as have been reported for several hormonal responses in animal systems.}, number={6}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Thompson, W. F. and Cleland, R.}, year={1971}, month={Dec}, pages={663–670} }
 @inbook{cleland_thompson_haughton_rayle_1971, title={Macromolecule synthesis and wall extensibility in relation to the mechanism of auxin-induced cell elongation}, booktitle={Plant Growth Substances 1970, VII International Congress on Plant Growth Substances}, author={Cleland, R. and Thompson, W.F. and Haughton, P.M. and Rayle, D.L.}, year={1971} }