@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{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} }
 @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{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={AbstractGenome integrity in eukaryotes depends on licensing mechanisms that prevent loading of the minichromosome maintenance complex (MCM2-7) onto replicated DNA during S phase. Although the principle of licensing appears to be conserved across all eukaryotes, the mechanisms that control it vary, and it is not clear how licensing is regulated in plants. In this work, we demonstrate that subunits of the MCM2-7 complex are coordinately expressed during Arabidopsis (Arabidopsis thaliana) development and are abundant in proliferating and endocycling tissues, indicative of a role in DNA replication. We show that endogenous MCM5 and MCM7 proteins are localized in the nucleus during G1, S, and G2 phases of the cell cycle and are released into the cytoplasmic compartment during mitosis. We also show that MCM5 and MCM7 are topologically constrained on DNA and that the MCM complex is stable under high-salt conditions. Our results are consistent with a conserved replicative helicase function for the MCM complex in plants but not with the idea that plants resemble budding yeast by actively exporting the MCM complex from the nucleus to prevent unauthorized origin licensing and rereplication during S phase. Instead, our data show that, like other higher eukaryotes, the MCM complex in plants remains in the nucleus throughout most of the cell cycle and is only dispersed in mitotic cells.}, 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} }
 @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{ascencio-ibanez_sozzani_lee_chu_wolfinger_cella_hanley-bowdoin_2008, title={Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection}, volume={148}, number={1}, journal={Plant Physiology}, author={Ascencio-Ibanez, J. T. and Sozzani, R. and Lee, T. J. and Chu, T. M. and Wolfinger, R. D. and Cella, R. and Hanley-Bowdoin, L.}, year={2008}, pages={436–454} }