@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{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{brooks_danehower_murphy_reberg-horton_burton_2012, title={Estimation of heritability of benzoxazinoid production in rye (Secale cereale) using gas chromatographic analysis}, volume={131}, ISSN={["1439-0523"]}, DOI={10.1111/j.1439-0523.2011.01885.x}, abstractNote={With 4 tables}, number={1}, journal={PLANT BREEDING}, publisher={Wiley}, author={Brooks, Ashley M. and Danehower, David A. and Murphy, J. Paul and Reberg-Horton, S. Chris and Burton, James D.}, year={2012}, month={Feb}, pages={104–109} }