TY - JOUR AU - Du, J. AU - Johnson, L. M. AU - Jacobsen, S. E. AU - Patel, D. J. PY - 2015 DA - 2015// TI - DNA methylation pathways and their crosstalk with histone methylation JO - Nat Rev Mol Cell Biol VL - 16 UR - https://doi.org/10.1038/nrm4043 DO - 10.1038/nrm4043 ID - Du2015 ER - TY - JOUR AU - Zemach, A. AU - Kim, M. Y. AU - Hsieh, P. -. H. AU - Coleman-Derr, D. AU - Eshed-Williams, L. AU - Thao, K. PY - 2013 DA - 2013// TI - The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin JO - Cell. VL - 153 UR - https://doi.org/10.1016/j.cell.2013.02.033 DO - 10.1016/j.cell.2013.02.033 ID - Zemach2013 ER - TY - JOUR AU - Stroud, H. AU - Do, T. AU - Du, J. AU - Zhong, X. AU - Feng, S. AU - Johnson, L. PY - 2014 DA - 2014// TI - Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis JO - Nat Struct Mol Biol VL - 21 UR - https://doi.org/10.1038/nsmb.2735 DO - 10.1038/nsmb.2735 ID - Stroud2014 ER - TY - JOUR AU - Raynaud, C. AU - Sozzani, R. AU - Glab, N. AU - Domenichini, S. AU - Perennes, C. AU - Cella, R. PY - 2006 DA - 2006// TI - Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis JO - Plant J VL - 47 UR - https://doi.org/10.1111/j.1365-313X.2006.02799.x DO - 10.1111/j.1365-313X.2006.02799.x ID - Raynaud2006 ER - TY - JOUR AU - Jacob, Y. AU - Feng, S. AU - LeBlanc, C. A. AU - Bernatavichute, Y. V. AU - Stroud, H. AU - Cokus, S. PY - 2009 DA - 2009// TI - ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing JO - Nat Struct Mol Biol VL - 16 UR - https://doi.org/10.1038/nsmb.1611 DO - 10.1038/nsmb.1611 ID - Jacob2009 ER - TY - JOUR AU - Yelagandula, R. AU - Stroud, H. AU - Holec, S. AU - Zhou, K. AU - Feng, S. AU - Zhong, X. PY - 2014 DA - 2014// TI - The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis JO - Cell. VL - 158 UR - https://doi.org/10.1016/j.cell.2014.06.006 DO - 10.1016/j.cell.2014.06.006 ID - Yelagandula2014 ER - TY - JOUR AU - Rigal, M. AU - Mathieu, O. PY - 2011 DA - 2011// TI - A “mille-feuille” of silencing: epigenetic control of transposable elements JO - Biochim Biophys Acta - Gene Regul Mech VL - 1809 UR - https://doi.org/10.1016/j.bbagrm.2011.04.001 DO - 10.1016/j.bbagrm.2011.04.001 ID - Rigal2011 ER - TY - JOUR AU - Fransz, P. AU - Hoopen, R. AU - Tessadori, F. PY - 2006 DA - 2006// TI - Composition and formation of heterochromatin in Arabidopsis thaliana JO - Chromosom Res VL - 14 UR - https://doi.org/10.1007/s10577-005-1022-5 DO - 10.1007/s10577-005-1022-5 ID - Fransz2006 ER - TY - JOUR AU - Soppe, W. J. J. AU - Jasencakova, Z. AU - Houben, A. AU - Kakutani, T. AU - Meister, A. AU - Huang, M. S. PY - 2002 DA - 2002// TI - DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis JO - EMBO J VL - 21 UR - https://doi.org/10.1093/emboj/cdf657 DO - 10.1093/emboj/cdf657 ID - Soppe2002 ER - TY - JOUR AU - Feng, W. AU - Hale, C. J. AU - Over, R. S. AU - Cokus, S. J. AU - Jacobsen, S. E. AU - Michaels, S. D. PY - 2017 DA - 2017// TI - Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage JO - Proc Natl Acad Sci VL - 114 UR - https://doi.org/10.1073/pnas.1619774114 DO - 10.1073/pnas.1619774114 ID - Feng2017 ER - TY - JOUR AU - Hale, C. J. AU - Potok, M. E. AU - Lopez, J. AU - Do, T. AU - Liu, A. AU - Gallego-Bartolome, J. PY - 2016 DA - 2016// TI - Identification of multiple proteins coupling transcriptional gene silencing to genome stability in Arabidopsis thaliana JO - Plos Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006092 DO - 10.1371/journal.pgen.1006092 ID - Hale2016 ER - TY - JOUR AU - Stroud, H. AU - Hale, C. J. AU - Feng, S. AU - Caro, E. AU - Jacob, Y. AU - Michaels, S. D. PY - 2012 DA - 2012// TI - DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1002808 DO - 10.1371/journal.pgen.1002808 ID - Stroud2012 ER - TY - JOUR AU - Kapoor, A. AU - Agarwal, M. AU - Andreucci, A. AU - Zheng, X. AU - Gong, Z. AU - Hasegawa, P. M. PY - 2005 DA - 2005// TI - Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA- methylation-independent manner in Arabidopsis JO - Curr Biol VL - 15 UR - https://doi.org/10.1016/j.cub.2005.09.013 DO - 10.1016/j.cub.2005.09.013 ID - Kapoor2005 ER - TY - JOUR AU - Liu, J. AU - Ren, X. AU - Yin, H. AU - Wang, Y. AU - Xia, R. AU - Wang, Y. PY - 2009 DA - 2009// TI - Mutation in the catalytic subunit of DNA polymerase α influences transcriptional gene silencing and homologous recombination in Arabidopsis JO - Plant J VL - 61 UR - https://doi.org/10.1111/j.1365-313X.2009.04026.x DO - 10.1111/j.1365-313X.2009.04026.x ID - Liu2009 ER - TY - JOUR AU - Yin, H. AU - Zhang, X. AU - Liu, J. AU - Wang, Y. AU - He, J. AU - Yang, T. PY - 2009 DA - 2009// TI - Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis JO - Plant Cell VL - 21 UR - https://doi.org/10.1105/tpc.108.061549 DO - 10.1105/tpc.108.061549 ID - Yin2009 ER - TY - JOUR AU - Zhang, J. AU - Xie, S. AU - Zhu, J. -. K. AU - Gong, Z. PY - 2016 DA - 2016// TI - Requirement for flap endonuclease 1 ( FEN1) to maintain genomic stability and transcriptional gene silencing in Arabidopsis JO - Plant J VL - 87 UR - https://doi.org/10.1111/tpj.13224 DO - 10.1111/tpj.13224 ID - Zhang2016 ER - TY - JOUR AU - Zhang, J. AU - Xie, S. AU - Cheng, J. AU - Lai, J. AU - Zhu, J. -. K. AU - Gong, Z. PY - 2016 DA - 2016// TI - The second subunit of DNA polymerase delta is required for genomic stability and epigenetic regulation JO - Plant Physiol VL - 171 ID - Zhang2016 ER - TY - JOUR AU - Takeda, S. AU - Tadele, Z. AU - Hofmann, I. AU - Probst, A. V. AU - Angelis, K. J. AU - Kaya, H. PY - 2004 DA - 2004// TI - BRU1, a novel link between responses to DNA damage and epigenetic gene silencing in Arabidopsis JO - Genes Dev VL - 18 UR - https://doi.org/10.1101/gad.295404 DO - 10.1101/gad.295404 ID - Takeda2004 ER - TY - JOUR AU - Elmayan, T. AU - Proux, F. AU - Vaucheret, H. PY - 2005 DA - 2005// TI - Arabidopsis RPA2: a genetic link among transcriptional gene silencing, DNA repair, and DNA replication JO - Curr Biol VL - 15 UR - https://doi.org/10.1016/j.cub.2005.09.044 DO - 10.1016/j.cub.2005.09.044 ID - Elmayan2005 ER - TY - JOUR AU - Liu, Q. AU - Wang, J. AU - Miki, D. AU - Xia, R. AU - Yu, W. AU - He, J. PY - 2010 DA - 2010// TI - DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis JO - Plant Cell VL - 22 UR - https://doi.org/10.1105/tpc.110.076349 DO - 10.1105/tpc.110.076349 ID - Liu2010 ER - TY - JOUR AU - Kirik, V. AU - Schrader, A. AU - Uhrig, J. F. AU - Hulskamp, M. PY - 2007 DA - 2007// TI - MIDGET unravels functions of the Arabidopsis topoisomerase VI complex in DNA endoreduplication, chromatin condensation, and transcriptional silencing JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.054361 DO - 10.1105/tpc.107.054361 ID - Kirik2007 ER - TY - JOUR AU - Stroud, H. AU - Greenberg, M. V. C. AU - Feng, S. AU - Bernatavichute, Y. V. AU - Jacobsen, S. E. PY - 2013 DA - 2013// TI - Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome JO - Cell. VL - 152 UR - https://doi.org/10.1016/j.cell.2012.10.054 DO - 10.1016/j.cell.2012.10.054 ID - Stroud2013 ER - TY - JOUR AU - Hyun, Y. AU - Yun, H. AU - Park, K. AU - Ohr, H. AU - Lee, O. AU - Kim, D. -. H. PY - 2013 DA - 2013// TI - The catalytic subunit of Arabidopsis DNA polymerase α ensures stable maintenance of histone modification JO - Development. VL - 140 UR - https://doi.org/10.1242/dev.084624 DO - 10.1242/dev.084624 ID - Hyun2013 ER - TY - JOUR AU - Olmo, I. AU - López, J. A. AU - Vázquez, J. AU - Raynaud, C. AU - Piñeiro, M. AU - Jarillo, J. A. PY - 2016 DA - 2016// TI - Arabidopsis DNA polymerase ϵ recruits components of Polycomb repressor complex to mediate epigenetic gene silencing JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw156 DO - 10.1093/nar/gkw156 ID - Olmo2016 ER - TY - JOUR AU - Iglesias, F. M. AU - Bruera, N. A. AU - Dergan-Dylon, S. AU - Marino-Buslje, C. AU - Lorenzi, H. AU - Mateos, J. L. PY - 2015 DA - 2015// TI - The arabidopsis DNA polymerase $δ$ has a role in the deposition of transcriptionally active epigenetic marks, development and flowering JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1004975 DO - 10.1371/journal.pgen.1004975 ID - Iglesias2015 ER - TY - JOUR AU - Roudier, F. AU - Ahmed, I. AU - Bérard, C. AU - Sarazin, A. AU - Mary-Huard, T. AU - Cortijo, S. PY - 2011 DA - 2011// TI - Integrative epigenomic mapping defines four main chromatin states in Arabidopsis JO - EMBO J VL - 30 UR - https://doi.org/10.1038/emboj.2011.103 DO - 10.1038/emboj.2011.103 ID - Roudier2011 ER - TY - JOUR AU - Jahn, L. J. AU - Mason, B. AU - Brøgger, P. AU - Toteva, T. AU - Nielsen, D. K. AU - Thon, G. PY - 2018 DA - 2018// TI - Dependency of heterochromatin domains on replication factors JO - G3 VL - 8 UR - https://doi.org/10.1534/g3.117.300341 DO - 10.1534/g3.117.300341 ID - Jahn2018 ER - TY - JOUR AU - Toteva, T. AU - Mason, B. AU - Kanoh, Y. AU - Brøgger, P. AU - Green, D. AU - Verhein-Hansen, J. PY - 2017 DA - 2017// TI - Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast JO - Proc Natl Acad Sci VL - 114 UR - https://doi.org/10.1073/pnas.1614837114 DO - 10.1073/pnas.1614837114 ID - Toteva2017 ER - TY - JOUR AU - Natsume, T. AU - Tsutsui, Y. AU - Sutani, T. AU - Dunleavy, E. M. AU - Pidoux, A. L. AU - Iwasaki, H. PY - 2008 DA - 2008// TI - A DNA polymerase α accessory protein, Mcl1, is required for propagation of centromere structures in fission yeast. Aramayo R, editor JO - Plos One VL - 3 UR - https://doi.org/10.1371/journal.pone.0002221 DO - 10.1371/journal.pone.0002221 ID - Natsume2008 ER - TY - JOUR AU - Nikolov, I. AU - Taddei, A. PY - 2016 DA - 2016// TI - Linking replication stress with heterochromatin formation JO - Chromosoma. VL - 125 UR - https://doi.org/10.1007/s00412-015-0545-6 DO - 10.1007/s00412-015-0545-6 ID - Nikolov2016 ER - TY - JOUR AU - Santos-Pereira, J. M. AU - Aguilera, A. PY - 2015 DA - 2015// TI - R loops: new modulators of genome dynamics and function JO - Nat Rev Genet VL - 16 UR - https://doi.org/10.1038/nrg3961 DO - 10.1038/nrg3961 ID - Santos-Pereira2015 ER - TY - JOUR AU - Morel, J. B. AU - Mourrain, P. AU - Béclin, C. AU - Vaucheret, H. PY - 2000 DA - 2000// TI - DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis JO - Curr Biol VL - 10 UR - https://doi.org/10.1016/S0960-9822(00)00862-9 DO - 10.1016/S0960-9822(00)00862-9 ID - Morel2000 ER - TY - JOUR AU - Tittel-Elmer, M. AU - Bucher, E. AU - Broger, L. AU - Mathieu, O. AU - Paszkowski, J. AU - Vaillant, I. PY - 2010 DA - 2010// TI - Stress-induced activation of heterochromatic transcription. Barsh GS, editor JO - Plos Genet VL - 6 UR - https://doi.org/10.1371/journal.pgen.1001175 DO - 10.1371/journal.pgen.1001175 ID - Tittel-Elmer2010 ER - TY - JOUR AU - Bourguet, P. AU - Bossoreille, S. AU - López-González, L. AU - Pouch-Pélissier, M. -. N. AU - Gómez-Zambrano, Á. AU - Devert, A. PY - 2018 DA - 2018// TI - A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing JO - Life Sci Alliance VL - 1 UR - https://doi.org/10.26508/lsa.201800197 DO - 10.26508/lsa.201800197 ID - Bourguet2018 ER - TY - JOUR AU - Ikeda, Y. AU - Pélissier, T. AU - Bourguet, P. AU - Becker, C. AU - Pouch-Pélissier, M. -. N. AU - Pogorelcnik, R. PY - 2017 DA - 2017// TI - Arabidopsis proteins with a transposon-related domain act in gene silencing JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/ncomms15122 DO - 10.1038/ncomms15122 ID - Ikeda2017 ER - TY - JOUR AU - Olmo, I. AU - López-González, L. AU - Martín-Trillo, M. M. AU - Martínez-Zapater, J. M. AU - Piñeiro, M. AU - Jarillo, J. A. PY - 2010 DA - 2010// TI - EARLY IN SHORT DAYS 7 (ESD7) encodes the catalytic subunit of DNA polymerase epsilon and is required for flowering repression through a mechanism involving epigenetic gene silencing JO - Plant J VL - 61 UR - https://doi.org/10.1111/j.1365-313X.2009.04093.x DO - 10.1111/j.1365-313X.2009.04093.x ID - Olmo2010 ER - TY - JOUR AU - Burgers, P. M. J. AU - Kunkel, T. A. PY - 2017 DA - 2017// TI - Eukaryotic DNA replication fork JO - Annu Rev Biochem VL - 86 UR - https://doi.org/10.1146/annurev-biochem-061516-044709 DO - 10.1146/annurev-biochem-061516-044709 ID - Burgers2017 ER - TY - JOUR AU - Han, Y. -. F. AU - Huang, H. -. W. AU - Li, L. AU - Cai, T. AU - Chen, S. AU - He, X. -. J. PY - 2015 DA - 2015// TI - The cytosolic iron-sulfur cluster assembly protein MMS19 regulates transcriptional gene silencing, DNA repair, and flowering time in Arabidopsis JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0129137 DO - 10.1371/journal.pone.0129137 ID - Han2015 ER - TY - STD TI - Wang H, Liu C, Cheng J, Liu J, Zhang L, He C, et al. Arabidopsis flower and embryo developmental genes are repressed in seedlings by different combinations of polycomb group proteins in association with distinct sets of cis-regulatory elements. Colot V, editor. Plos Genet. 2016 12(1):e1005771. ID - ref39 ER - TY - STD TI - Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X. EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nat Genet. 2018;50(9):1247–53. ID - ref40 ER - TY - JOUR AU - Pedroza-García, J. -. A. AU - Mazubert, C. AU - Olmo, I. AU - Bourge, M. AU - Domenichini, S. AU - Bounon, R. PY - 2017 DA - 2017// TI - Function of the plant DNA polymerase epsilon in replicative stress sensing, a genetic analysis JO - Plant Physiol VL - 173 UR - https://doi.org/10.1104/pp.17.00031 DO - 10.1104/pp.17.00031 ID - Pedroza-García2017 ER - TY - JOUR AU - Jacob, Y. AU - Stroud, H. AU - LeBlanc, C. AU - Feng, S. AU - Zhuo, L. AU - Caro, E. PY - 2010 DA - 2010// TI - Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases JO - Nature. VL - 466 UR - https://doi.org/10.1038/nature09290 DO - 10.1038/nature09290 ID - Jacob2010 ER - TY - JOUR AU - Ma, Z. AU - Castillo-González, C. AU - Wang, Z. AU - Sun, D. AU - Hu, X. AU - Shen, X. PY - 2018 DA - 2018// TI - Arabidopsis serrate coordinates histone methyltransferases ATXR5/6 and RNA processing factor RDR6 to regulate transposon expression JO - Dev Cell VL - 45 UR - https://doi.org/10.1016/j.devcel.2018.05.023 DO - 10.1016/j.devcel.2018.05.023 ID - Ma2018 ER - TY - JOUR AU - Osakabe, A. AU - Lorković, Z. J. AU - Kobayashi, W. AU - Tachiwana, H. AU - Yelagandula, R. AU - Kurumizaka, H. PY - 2018 DA - 2018// TI - Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gky540 DO - 10.1093/nar/gky540 ID - Osakabe2018 ER - TY - STD TI - Gouil Q, Baulcombe DC. DNA methylation signatures of the plant chromomethyltransferases. Mittelsten Scheid O, editor. Plos Genet. 2016 12(12):e1006526. ID - ref45 ER - TY - JOUR AU - Kaya, H. AU - Shibahara, K. AU - Taoka, K. AU - Iwabuchi, M. AU - Stillman, B. AU - Araki, T. PY - 2001 DA - 2001// TI - FASCIATA genes for chromatin assembly factor-1 in Arabidopsis maintain the cellular organization of apical meristems JO - Cell. VL - 104 UR - https://doi.org/10.1016/S0092-8674(01)00197-0 DO - 10.1016/S0092-8674(01)00197-0 ID - Kaya2001 ER - TY - JOUR AU - Mozgová, I. AU - Wildhaber, T. AU - Trejo-Arellano, M. S. AU - Fajkus, J. AU - Roszak, P. AU - Köhler, C. PY - 2018 DA - 2018// TI - Transgenerational phenotype aggravation in CAF-1 mutants reveals parent-of-origin specific epigenetic inheritance JO - New Phytol VL - 220 UR - https://doi.org/10.1111/nph.15082 DO - 10.1111/nph.15082 ID - Mozgová2018 ER - TY - JOUR AU - Schönrock, N. AU - Exner, V. AU - Probst, A. AU - Gruissem, W. AU - Hennig, L. PY - 2006 DA - 2006// TI - Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M513426200 DO - 10.1074/jbc.M513426200 ID - Schönrock2006 ER - TY - JOUR AU - Exner, V. AU - Taranto, P. AU - Schonrock, N. AU - Gruissem, W. AU - Hennig, L. PY - 2006 DA - 2006// TI - Chromatin assembly factor CAF-1 is required for cellular differentiation during plant development JO - Development. VL - 133 UR - https://doi.org/10.1242/dev.02599 DO - 10.1242/dev.02599 ID - Exner2006 ER - TY - JOUR AU - Ühlken, C. AU - Horvath, B. AU - Stadler, R. AU - Sauer, N. AU - Weingartner, M. PY - 2014 DA - 2014// TI - MAIN-LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana JO - Plant J VL - 78 UR - https://doi.org/10.1111/tpj.12455 DO - 10.1111/tpj.12455 ID - Ühlken2014 ER - TY - JOUR AU - Wenig, U. AU - Meyer, S. AU - Stadler, R. AU - Fischer, S. AU - Werner, D. AU - Lauter, A. PY - 2013 DA - 2013// TI - Identification of MAIN, a factor involved in genome stability in the meristems of Arabidopsis thaliana JO - Plant J VL - 75 UR - https://doi.org/10.1111/tpj.12215 DO - 10.1111/tpj.12215 ID - Wenig2013 ER - TY - JOUR AU - Singh, A. AU - Xu, Y. -. J. PY - 2016 DA - 2016// TI - The cell killing mechanisms of Hydroxyurea JO - Genes (Basel) VL - 7 UR - https://doi.org/10.3390/genes7110099 DO - 10.3390/genes7110099 ID - Singh2016 ER - TY - STD TI - Técher H, Koundrioukoff S, Nicolas A, Debatisse M. The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat Rev Genet. 2017. Rev Genet. 2017;18(9):535–50. ID - ref53 ER - TY - JOUR AU - Bonner, W. M. AU - Redon, C. E. AU - Dickey, J. S. AU - Nakamura, A. J. AU - Sedelnikova, O. A. AU - Solier, S. PY - 2008 DA - 2008// TI - GammaH2AX and cancer JO - Nat Rev Cancer VL - 8 UR - https://doi.org/10.1038/nrc2523 DO - 10.1038/nrc2523 ID - Bonner2008 ER - TY - JOUR AU - Iyer, D. AU - Rhind, N. PY - 2017 DA - 2017// TI - The intra-S checkpoint responses to DNA damage JO - Genes (Basel) VL - 8 UR - https://doi.org/10.3390/genes8020074 DO - 10.3390/genes8020074 ID - Iyer2017 ER - TY - JOUR AU - Talbert, P. B. AU - Henikoff, S. PY - 2010 DA - 2010// TI - Histone variants--ancient wrap artists of the epigenome JO - Nat Rev Mol Cell Biol. VL - 11 UR - https://doi.org/10.1038/nrm2861 DO - 10.1038/nrm2861 ID - Talbert2010 ER - TY - STD TI - Stroud H, Otero S, Desvoyes B, Ramirez-Parra E, Jacobsen SE, Gutierrez C. Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2012;109(14):5370–5375. ID - ref57 ER - TY - STD TI - Wollmann H, Holec S, Alden K, Clarke ND, Jacques P-É, Berger F. Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome. Kakutani T, editor. Plos Genet. 2012 8(5):e1002658. ID - ref58 ER - TY - JOUR AU - Wollmann, H. AU - Stroud, H. AU - Yelagandula, R. AU - Tarutani, Y. AU - Jiang, D. AU - Jing, L. PY - 2017 DA - 2017// TI - The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1221-3 DO - 10.1186/s13059-017-1221-3 ID - Wollmann2017 ER - TY - STD TI - Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife. 2017;6:e30674. ID - ref60 ER - TY - JOUR AU - Otero, S. AU - Desvoyes, B. AU - Peiro, R. AU - Gutierrez, C. PY - 2016 DA - 2016// TI - Histone H3 dynamics reveal domains with distinct proliferation potential in the Arabidopsis root JO - Plant Cell VL - 28 UR - https://doi.org/10.1105/tpc.15.01003 DO - 10.1105/tpc.15.01003 ID - Otero2016 ER - TY - JOUR AU - Benoit, M. AU - Simon, L. AU - Desset, S. AU - Duc, C. AU - Cotterell, S. AU - Poulet, A. PY - 2019 DA - 2019// TI - Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development JO - New Phytol VL - 221 UR - https://doi.org/10.1111/nph.15248 DO - 10.1111/nph.15248 ID - Benoit2019 ER - TY - JOUR AU - Du, J. AU - Zhong, X. AU - Bernatavichute, Y. V. AU - Stroud, H. AU - Feng, S. AU - Caro, E. PY - 2012 DA - 2012// TI - Dual Binding of Chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants JO - Cell. VL - 151 UR - https://doi.org/10.1016/j.cell.2012.07.034 DO - 10.1016/j.cell.2012.07.034 ID - Du2012 ER - TY - JOUR AU - Jenik, P. D. AU - Jurkuta, R. E. J. AU - Barton, M. K. PY - 2005 DA - 2005// TI - Interactions between the cell cycle and embryonic patterning in Arabidopsis uncovered by a mutation in DNA polymerase epsilon JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.105.036889 DO - 10.1105/tpc.105.036889 ID - Jenik2005 ER - TY - JOUR AU - Jasencakova, Z. AU - Scharf, A. N. D. AU - Ask, K. AU - Corpet, A. AU - Imhof, A. AU - Almouzni, G. PY - 2010 DA - 2010// TI - Replication stress interferes with histone recycling and predeposition marking of new histones JO - Mol Cell VL - 37 UR - https://doi.org/10.1016/j.molcel.2010.01.033 DO - 10.1016/j.molcel.2010.01.033 ID - Jasencakova2010 ER - TY - JOUR AU - Zaratiegui, M. PY - 2017 DA - 2017// TI - Cross-regulation between transposable elements and host DNA replication JO - Viruses. VL - 9 UR - https://doi.org/10.3390/v9030057 DO - 10.3390/v9030057 ID - Zaratiegui2017 ER - TY - JOUR AU - Lippman, Z. AU - Gendrel, A. -. V. AU - Black, M. AU - Vaughn, M. W. AU - Dedhia, N. AU - Richard McCombie, W. PY - 2004 DA - 2004// TI - Role of transposable elements in heterochromatin and epigenetic control JO - Nature. VL - 430 UR - https://doi.org/10.1038/nature02651 DO - 10.1038/nature02651 ID - Lippman2004 ER - TY - JOUR AU - Zhang, X. AU - Yazaki, J. AU - Sundaresan, A. AU - Cokus, S. AU - Chan, S. W. L. AU - Chen, H. PY - 2006 DA - 2006// TI - Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis JO - Cell. VL - 126 UR - https://doi.org/10.1016/j.cell.2006.08.003 DO - 10.1016/j.cell.2006.08.003 ID - Zhang2006 ER - TY - STD TI - Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell. 2020;77(2):310–323.e7. ID - ref69 ER - TY - JOUR AU - Mi, H. AU - Muruganujan, A. AU - Ebert, D. AU - Huang, X. AU - Thomas, P. D. PY - 2019 DA - 2019// TI - PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky1038 DO - 10.1093/nar/gky1038 ID - Mi2019 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics. VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Liao, Y. AU - Smyth, G. K. AU - Shi, W. PY - 2014 DA - 2014// TI - featureCounts: an efficient general purpose program for assigning sequence reads to genomic features JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt656 DO - 10.1093/bioinformatics/btt656 ID - Liao2014 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Bernatavichute, Y. V. AU - Zhang, X. AU - Cokus, S. AU - Pellegrini, M. AU - Jacobsen, S. E. PY - 2008 DA - 2008// TI - Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana JO - Plos One VL - 3 UR - https://doi.org/10.1371/journal.pone.0003156 DO - 10.1371/journal.pone.0003156 ID - Bernatavichute2008 ER - TY - STD TI - Gendrel AV, Lippman Z, Martienssen R, Colot V. Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods. 2005;2(3):213–8. ID - ref75 ER - TY - JOUR AU - Jégu, T. AU - Veluchamy, A. AU - Ramirez-Prado, J. S. AU - Rizzi-Paillet, C. AU - Perez, M. AU - Lhomme, A. PY - 2017 DA - 2017// TI - The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1246-7 DO - 10.1186/s13059-017-1246-7 ID - Jégu2017 ER - TY - JOUR AU - Feng, J. AU - Liu, T. AU - Qin, B. AU - Zhang, Y. AU - Liu, X. S. PY - 2012 DA - 2012// TI - Identifying ChIP-seq enrichment using MACS JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.101 DO - 10.1038/nprot.2012.101 ID - Feng2012 ER - TY - JOUR AU - Ramírez, F. AU - Dündar, F. AU - Diehl, S. AU - Grüning, B. A. AU - Manke, T. PY - 2014 DA - 2014// TI - deepTools: a flexible platform for exploring deep-sequencing data JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku365 DO - 10.1093/nar/gku365 ID - Ramírez2014 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics. VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - JOUR AU - Charbonnel, C. AU - Gallego, M. E. AU - White, C. I. PY - 2010 DA - 2010// TI - Xrcc1-dependent and Ku-dependent DNA double-strand break repair kinetics in Arabidopsis plants JO - Plant J VL - 64 UR - https://doi.org/10.1111/j.1365-313X.2010.04331.x DO - 10.1111/j.1365-313X.2010.04331.x ID - Charbonnel2010 ER - TY - STD TI - Schalk C, Drevensek S, Kramdi A, Kassam M, Ahmed I, Cognat V, Graindorge S, Bergdoll M, Baumberger N, Heintz D, Bowler C, Genschik P, Barneche F, Colot V, Molinier J. DNA DAMAGE BINDING PROTEIN2 Shapes the DNA Methylation Landscape. Plant Cell. 2016;28(9):2043–59. ID - ref81 ER - TY - STD TI - Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics. 2013;14:774. ID - ref82 ER - TY - STD TI - R Core Team. R: A language and environment for statistical computing. Vienna URL http://www.R-project.org/: R Found Stat Comput; 2019. UR - http://www.R-project.org/ ID - ref83 ER - TY - BOOK AU - Schneider, G. AU - Chicken, E. AU - Becvarik, R. PY - 2018 DA - 2018// TI - NSM3: functions and datasets to accompany Hollander, Wolfe, and Chicken - nonparametric statistical methods, Third Edition. R package version 1.12 ID - Schneider2018 ER - TY - STD TI - Bourguet P, Mathieu O. DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis. E-MTAB-8938, E-MTAB-8939, E-MTAB-8940, E-MTAB-9046. ArrayExpress. 2020. https://www.ebi.ac.uk/arrayexpress/. Accessed 18 Oct 2020. UR - https://www.ebi.ac.uk/arrayexpress/ ID - ref85 ER -