William F. Thompson

A protocol for genome-wide analysis of DNA replication timing in intact root tips

Methods in Molecular Biology Series.

Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

CURRENT BIOLOGY, 31(3), 591-+.

Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin(1)([OPEN])

PLANT PHYSIOLOGY, 183(1), 206–220.

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

PLOS GENETICS, 16(10).

Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L)

Turpin, Z. M., Vera, D. L., Savadel, S. D., Lung, P.-Y., Wear, E. E., Mickelson-Young, L., … Bass, H. W. (2018, October). DATA IN BRIEF, Vol. 20, pp. 358–363.

Genome-Wide Analysis of the Arabidopsis Replication Timing Program

PLANT PHYSIOLOGY, 176(3), 2166–2185.

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

PLANT CELL, 29(9), 2126–2149.

Repliscan: a tool for classifying replication timing regions

BMC BIOINFORMATICS, 18, 1–14.

A flow cytometric method for estimating S-phase duration in plants

JOURNAL OF EXPERIMENTAL BOTANY, 67(21), 6077–6087.

Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry

In Methods in Molecular Biology (pp. 69–86).

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

PLANT MOLECULAR BIOLOGY, 89(4-5), 339–351.

A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development

[Review of ]. JOURNAL OF EXPERIMENTAL BOTANY, 65(10), 2747–2756.

In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts

PLANT CELL, 26(1), 102–120.

Starch Self-Processing in Transgenic Sweet Potato Roots Expressing a Hyperthermophilic alpha-Amylase

BIOTECHNOLOGY PROGRESS, 27(2), 351–359.

Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State

PLoS Genetics, 6(6), e1000982.

Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants

PLANT PHYSIOLOGY, 150(2), 658–669.

Plant Genome Engineering Using Zinc Finger Nucleases

In Molecular Techniques in Crop Improvement (pp. 579–590).

Plant cell calcium-rich environment enhances thermostability of recombinantly produced α-amylase from the hyperthermophilic bacterium Thermotoga maritime

Biotechnology and Bioengineering, 104(5), 947–956.

Simultaneous excision of two transgene flanking sequences and resolution of complex integration loci

PLANT MOLECULAR BIOLOGY, 69(1-2), 23–32.

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

PLoS Biology, 6(12), e302.

Epigenomic consequences of immortalized plant cell suspension culture

[Review of ]. PLoS Biology, 6(12), 2880–2895.

Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice(1[W][OA])

[Review of ]. Plant Physiology, 144(4), 1697–1714.

A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide

NATURE PROTOCOLS, 1(5), 2320–2325.

Gene targeting in plants: fingers on the move

[Review of ]. TRENDS IN PLANT SCIENCE, 11(4), 159–161.

High efficiency gene targeting in plants

Washington, DC: U.S. Patent and Trademark Office.

In situ methods to localize transgenes and transcripts in interphase nuclei: a tool for transgenic plant research

Plant Methods, 2, 18.

A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue

PLANT MOLECULAR BIOLOGY REPORTER, 23(4), 405–409.

Matrix attachment regions and regulated transcription increase and stabilize transgene expression

PLANT BIOTECHNOLOGY JOURNAL, 3(5), 535–543.

Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to Tomato Spotted Wilt Virus in transgenic tobacco

TRANSGENIC RESEARCH, 14(2), 193–206.

The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: A flow cytometric study

PLANT CELL, 17(2), 418–429.

Establishment of rapidly proliferating rice cell suspension culture and its characterization by fluorescence-activated cell sorting analysis

PLANT MOLECULAR BIOLOGY REPORTER, 22(3), 259–267.

Transgene Integration: Use of Matrix Attachment Regions

In Transgenic Plants (pp. 313–326).

Analysis of trans-silencing interactions using transcriptional silencers of varying strength and targets with and without flanking nuclear matrix attachment regions

TRANSGENIC RESEARCH, 12(3), 305–318.

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

TRANSGENIC RESEARCH, 12(1), 3–12.

Differential Top10 promoter regulation by six tetracycline analogues in plant cells

JOURNAL OF EXPERIMENTAL BOTANY, 53(376), 1871–1877.

High-throughput transgene copy number estimation by competitive PCR

PLANT MOLECULAR BIOLOGY REPORTER, 20(3), 265–277.

Up-regulation of phosphoinositide metabolism in tobacco cells constitutively expressing the human type I inositol polyphosphate 5-phosphatase

PLANT PHYSIOLOGY, 129(4), 1795–1806.

When a day makes a difference. Interpreting data from endoplasmic reticulum-targeted green fluorescent protein fusions in cells grown in suspension culture

Plant Physiology, 128(2), 341–344.

When a day makes a difference. Interpreting data from endoplasmic reticulum-targeted green fluorescent protein fusions in cells grown in suspension culture

Plant Physiology, 128(2), 341–344.

Generation of Intron-Containing, ER-Localized, Soluble-Modified Green Fluorescent Protein Genes for use in Plant Transformation

Plant Molecular Biology Reporter, 19(1), 13–26.

Method for reducing expression variability of transgenes in plant cells

Washington, DC: U.S. Patent and Trademark Office.

The 5 ' end of the pea ferredoxin-1 mRNA mediates rapid and reversible light-directed changes in translation in tobacco

PLANT PHYSIOLOGY, 125(2), 770–778.

The Ca2+ status of the endoplasmic reticulum is altered by induction of calreticulin expression in transgenic plants

PLANT PHYSIOLOGY, 126(3), 1092–1104.

The role of cell differentiation state and HMG-I/Y in the expression of transgenes flanked by matrix attachment regions

TRANSGENIC RESEARCH, 10(5), 465–470.

Heat shock protein HSP101 binds to the Fed-1 internal light regulatory element and mediates its high translational activity

PLANT CELL, 12(7), 1213–1227.

Increasing expression of transgenes in plant cells using insulator elements

Washington, DC: U.S. Patent and Trademark Office.

Method for reducing expression variability of transgenes in plant cells

Washington, DC: U.S. Patent and Trademark Office.

Post-Transcriptional Light Regulation of Nuclear-Encoded Genes

In Genetic Engineering (pp. 1–10).

Premature termination codons destabilize ferredoxin-1 mRNA when ferredoxin-1 is translated

PLANT JOURNAL, 21(6), 563–569.

Stringent control of transgene expression in Arabidopsis thaliana using the Top10 promoter system

PLANT JOURNAL, 21(6), 579–588.

Use of matrix attachment regions (MARs) to minimize transgene silencing

[Review of ]. PLANT MOLECULAR BIOLOGY, 43(2-3), 361–376.

A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants

PLANT JOURNAL, 18(3), 253–263.

Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants

BIOCHEMISTRY, 38(39), 12795–12804.

Matrix attachment regions increase transgene expression levels and stability in transgenic rice plants and their progeny

PLANT JOURNAL, 18(3), 233–242.

Transposon tagging of the sulfur gene of tobacco using engineered maize Ac/Ds elements

Genetics, 153(4), 1919–1928.

Ferredoxin-1 mRNA is destabilized by changes in photosynthetic electron transport

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 95(15), 9009–9013.

Gene silencing from plant DNA carried by a Geminivirus

PLANT JOURNAL, 14(1), 91–100.

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

Physiologia Plantarum, 103(3), 377–384.

Light regulation of Fed-1 mRNA requires an element in the 5' untranslated region and correlates with differential polyribosome association

Plant Cell, 10(3), 475–484.

Method of increasing expression for foreign genes in plant cells

Washington, DC: U.S. Patent and Trademark Office.

Plant nuclear scaffold attachment region and method for increasing gene expression in transgenic cells

Washington, DC: U.S. Patent and Trademark Office.

The dependence of Fed-1 light regulation on translation

In J. Bailey-Serres & D. R. Gallie (Eds.), A look beyond transcription: Mechanisms determining mRNAstability and translation in plants (pp. 96–101). Washington, DC: American Society of Plant Physiologists.

Characterization of post transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco

Plant Cell, 9(8), 1411–1423.

Introduction of a plant intron into the luciferase gene of Photinus pyralis

Plant Molecular Biology Reporter, 15(2), 186–196.

Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis

Plant Cell, 9(12), 2291–2300.

Sites of rDNA transcription are widely

Plant Journal, 12(1997), 571–581.

The dark-adaptation response of the de-etiolated pea mutant lip1 is modulated by external signals and endogenous programs

PLANT PHYSIOLOGY, 115(1), 23–28.

High-Level Transgene Expression in Plant Cells: Effects of a Strong Scaffold Attachment Region from Tobacco

The Plant Cell, 8(5), 899.

Matrix Attachment Regions and Transgene Expression

In Genomes of Plants and Animals (pp. 243–269).

Nuclear Matrix Attachment Regions and Transgene Expression in Plants

Plant Physiology, 110(1), 15–21.

Post-transcriptional regulation by light

In W. R. Briggs, R. L. Heath, & E. M. Tobin (Eds.), Regulation of Plant Growth and Development by Light. Rockville, MD: American Society of Plant Physiologists.

A nuclear scaffold attachment region from tobacco greatly increases transgene expression in plant cells

In R. Phillips & K. Oono (Eds.), Proceedings of the US-Japan Symposium on Modification of Gene Expression and Non-Mendelian Inheritance (pp. 281–295).

Individual Members of the Cab Gene Family Differ Widely in Fluence Response

Plant Physiology, 107(1), 161–165.

Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site

Plant Molecular Biology, 27(1), 27–39.

Light modulation of ferredoxin mRNA abundance requires an open reading frame

Plant Cell, 6, 1171–1176.

Spotlight on phytochrome nomenclature

Plant Cell, 6, 468–471.

Ferredoxin gene expression and its regulation by light

In D. P. S. Verma (Ed.), Control of Plant Gene Expression (pp. 211–222). Boca Raton, FL: CRC Press.

Scaffold attachment regions increase reporter gene expresssion in stably transformed plant cells

Plant Cell, 5(6), 603–613.

Sequence of Lhcb3∗1, a gene encoding a Photosystem II chlorophyll protein in Pisum

Biochimica Et Biophysica Acta (BBA) - Gene Structure and Expression, 1173(3), 333–336.

Both internal and external elements control expression of the pea Fed-1 gene in etiolated seedlings

Plant Cell, 4, 389–395.

Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac

Plant Molecular Biology, 20(2), 177–198.

Expression of the chlorophyll-a/b-protein multigene family in pea (Pisum sativum L.)

Planta, 188(2), 190–198.

Ferredoxin gene expression and its regulation by light

In D. P. S. Verma (Ed.), Control of Gene Expression (pp. 211–222). CRC Press.

Initial characterization of a pea mutant with light-independent photomorphogenesis

Plant Cell, 4(12), 1519–1530.

Light regulatory sequences are located within the 5' portion of the Fed-1 message sequence

EMBO Journal, 11(6), 2311–2317.

The pea ferredoxin I gene exhibits different light responses in etiolated seedlings of pea and tobacco

Plant Cell, 4, 383–388.

Concatemer chain reaction: A taq DNA polymerase-mediated mechanism for generating long tandemly repetitive DNA sequences

Analytical Biochemistry, 199(2), 184–190.

High mobility group chromosomal proteins bind to AT-rich tracts flanking plant genes

Plant Molecular Biology, 16(1), 95–104.

Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica

Journal of Protozoology, 38(2), 129–135.

Nuclear scaffold and scaffold attachment regions (SARs) in higher plants

Proceedings of the National Academy of Sciences of United States of America, 88(20), 9320–9324.

Nucleotide sequence ofCab-215, a Type II gene encoding a photosystem II chlorophylla/b-binding protein inPisum

Plant Molecular Biology, 17(1), 135–139.

Nucleotide sequence ofCab-8, a new type I gene encoding a chlorophylla/b-binding protein of LHC II inPisum

Plant Molecular Biology, 17(3), 523–526.

PHYSIOLOGICAL AND MOLECULAR STUDIES OF LIGHT-REGULATED NUCLEAR GENES IN HIGHER-PLANTS

[Review of ]. ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY, 42, 423–466.

The Inheritance and Linkage Mapping of Ferredoxin-1 in Pea

Journal of Heredity, 82(3), 259–261.

Unusual Features of the Light Response System Regulating Ferredoxin Gene Expression

In Phytochrome Properties and Biological Action (pp. 201–216).

Light regulated expression of the Fed-1 gene in pea involves cis-acting elements within the transcription unit

Monograph (British Society for Plant Growth Regulation), (20), 3.

Light regulated expression of the Fed-1 gene in pea involves cis-acting elements within the transcription unit

In T. Thomas & A. Smith (Eds.), British Society for Plant Growth Regulation, Monograph 20, Mechanisms of Plant Perception and Response to Environmental Stimuli (pp. 3–17).

A developmentally regulated bud specific mRNA sequence in pea has sequence similarity to seed lectins

Plant Physiology, 89(3), 833–838.

Characterization of a single copy gene encoding ferredoxin I from pea

The Plant Cell, 1, 681–690.

Chloroplast gene expression in lettuce grown under different irradiances

Planta, 178(1), 69–75.

Cis-acting elements for light regulation of pea ferredoxin I gene expression are located within transcribed sequences

The Plant Cell, 1, 691–698.

The identification and localization of 33 pea chloroplast transcription initiation sites

Current Genetics, 16(5-6), 433–445.

A transcription map of the pea chloroplast genome

Current Genetics, 14(1), 75–89.

Chromatin structure and expression of plant ribosomal RNA genes

In G. Kahl (Ed.), Architecture of Eukaryotic Genes (pp. 385–396). Weinheim: VCH Verlagsgesellschaft.

Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat

Journal of Molecular Biology, 204, 500–534.

DNase I sensitivity of ribosomal RNA Genes in chromatin and nucleolar dominance in wheat

Journal of Molecular Biology, 204(3), 535–548.

Inversions in legume chloroplast DNAs

Current Genetics, 14, 65–74.

Light Effects on Several Chloroplast Components in Norflurazon-Treated Pea Seedlings

PLANT PHYSIOLOGY, 88(2), 340–347.

Molecular Plant Development

Englewood Cliffs, NJ: Prentice Hall.

Nuclear-Cytoplasmic Partitioning of Phytochrome-Regulated Transcripts in Pisum sativum

PLANT PHYSIOLOGY, 88(4), 1397–1402.

Patterns of phytochrome-induced gene expression in etiolated pea buds

In Biomechanisms Regulating Growth and Development (pp. 269–284).

Photoregulation: diverse gene responses in greening seedlings

Plant, Cell and Environment, 11(5), 319–328.

Phytochrome Regulation of Greening in Pisum: Chlorophyll Accumulation and Abundance of mRNA for the Light-Harvesting Chlorophyll a/b Binding Proteins

PLANT PHYSIOLOGY, 86(1), 299–305.

Purification and restriction endonuclease analysis of plant nuclear DNA

In A. Weissbach & H. Weissbach (Eds.), Methods for Plant Molecular Biology. Orlando FL: Academic Press.

A phytochrome-regulated transcript encodes ferredoxin in Pisum sativum

Plant Molecular Biology, 8, 53–59.

Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements

Current Genetics, 11(4), 275–286.

Developmental regulation of cytosine methylation in the nuclear ribosomal RNA genes of Pisum sativum

Journal of Molecular Biology, 193(1), 15–26.

Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum

Proceedings of the National Academy of Sciences, 84(6), 1550–1554.

Specific mRNA and rRNA Levels in Greening Pea Leaves during Recovery from Iron Stress

PLANT PHYSIOLOGY, 84(2), 409–414.

Structure and variation in ribosomal RNA genes of pea: Characterization of a cloned rDNA repeat and chromosomal rDNA variants

Plant Molecular Biology, 8(1), 3–12.

Distribution, inheritance and linkage relationships of ribosomal DNA spacer length variants in pea

Theoretical and Applied Genetics, 72(3), 289–295.

Phytochrome Control of Specific mRNA levels in Developing Pea Buds : Kinetics of Accumulation, Reciprocity, and Escape Kinetics of the Low Fluence Response

PLANT PHYSIOLOGY, 81(4), 1033–1038.

Purification and restriction endonuclease analysis of plant nuclear DNA

Methods in Enzymology, 118, 57–75.

Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda

Current Genetics, 10(11), 835–841.

The differential expression of ribosomal RNA genes

Philosophical Transactions of Royal Society of London, B314(1166), 385–397.

The watermelon mitochondrial URF-1 gene: evidence for a complex structure

Current Genetics, 10(11), 857–869.

Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis

Genetics, 109, 195–213.

Chromosome architecture: the distribution of recombination sites, the structure of ribosomal DNA loci, and the multiplicity of sequences containing inverted repeats

In L. van Vloten-Doting, G. S. P. Groot, & T. C. Hall (Eds.), Molecular Form and Function of the Plant Genome. New York: Plenum Press.

Induction of plant gene expression by light

BioEssays, 3(4), 153–159.

Inheritance, organization, and mapping of rbcS and cab multigene families in pea

Proceedings of the National Academy of Sciences, 82(15), 5083–5087.

Photoregulation of nuclear-encoded transcripts: blue light regulation of specific transcript abundance

In K. E. Steinback, S. Bonitz, C. J. Arntzen, & L. Bogorad (Eds.), The Molecular Biology of the Photosynthetic Aparatus (pp. 367–376).

Phytochrome Control of Specific mRNA Levels in Developing Pea Buds : The Presence of Both Very Low Fluence and Low Fluence Responses

PLANT PHYSIOLOGY, 78(2), 388–393.

Phytochrome Regulation of Plant Development at the Whole Plant, Physiological, and Molecular Levels

In Sensory Perception and Transduction in Aneural Organisms (pp. 265–280).

Different red light requirements for phytochrome-induced accumulation of Cab RNA and RbcS RNA

Science, 226(4681), 1447–1449.

Evolutionary aspects of chloroplast genome expression and organization

In R. Hallick, L. A. Staehelin, J. P. Thornber, & A. R. Liss (Eds.), Biosynthesis of the Photosynthetic Apparatus: Molecular Biology, Development and Regulation (Vol. 14, pp. 273–283). New York: UCLA Symposia on Molecular and Cellular Biology, New Series.

Chloroplast genes for components of the translational apparatus

In Carnegie Institution Washington Year Book (Vol. 82, pp. 24–26).

Cytosine methylation of ribosomal RNA genes and nucleolus organizer activity in wheat

Proceedings of the Kew Chromosome Conference II, 11–17.

DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants.

Proceedings of the National Academy of Sciences, 80(3), 815–819.

Mitochondrial DNA sequence evolution and homology to chloroplast DNA in angiosperms

UCLA Symposia on Molecular and Cellular Biology, 12, 467–477.

Phytochrome control of RNA levels in developing pea and mung-bean leaves

Planta, 158(6), 487–500.

Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost

Cell, 29(2), 537–550.