Daniel Zilberman

Zilberman Group

48 Publications

Mark all

[48]
2023 | Journal Article | IST-REx-ID: 12672 | OA
Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132
[Published Version] View | Files available | DOI | WoS
 
[47]
2023 | Journal Article | IST-REx-ID: 14551 | OA
Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[46]
2023 | Journal Article | IST-REx-ID: 13965 | OA
Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 2023;81(8). doi:10.1016/j.gde.2023.102087
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[45]
2021 | Journal Article | IST-REx-ID: 9877 | OA
Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[44]
2021 | Journal Article | IST-REx-ID: 10533 | OA
Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[43]
2020 | Journal Article | IST-REx-ID: 9526 | OA
Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. 2020;77(2):310-323.e7. doi:10.1016/j.molcel.2019.10.011
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[42]
2019 | Journal Article | IST-REx-ID: 9460 | OA
Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[41]
2019 | Journal Article | IST-REx-ID: 9530 | OA
Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[40]
2018 | Journal Article | IST-REx-ID: 9471 | OA
Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[39]
2017 | Journal Article | IST-REx-ID: 9445 | OA
Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[38]
2017 | Journal Article | IST-REx-ID: 9506 | OA
Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[37]
2016 | Journal Article | IST-REx-ID: 9456 | OA
Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[36]
2016 | Journal Article | IST-REx-ID: 9477 | OA
Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[35]
2016 | Journal Article | IST-REx-ID: 9473 | OA
Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[34]
2015 | Journal Article | IST-REx-ID: 9532 | OA
Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[33]
2014 | Journal Article | IST-REx-ID: 9519
Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
View | DOI | PubMed | Europe PMC
 
[32]
2014 | Journal Article | IST-REx-ID: 9458 | OA
Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[31]
2014 | Journal Article | IST-REx-ID: 9479 | OA
Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[30]
2013 | Journal Article | IST-REx-ID: 9459 | OA
Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[29]
2013 | Journal Article | IST-REx-ID: 9481 | OA
Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939. doi:10.1073/pnas.1306164110
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[28]
2013 | Journal Article | IST-REx-ID: 9520 | OA
Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[27]
2012 | Journal Article | IST-REx-ID: 9451 | OA
Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[26]
2012 | Journal Article | IST-REx-ID: 9535 | OA
Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[25]
2012 | Journal Article | IST-REx-ID: 9499 | OA
Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 9497 | OA
Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[23]
2012 | Journal Article | IST-REx-ID: 9528
Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007
View | DOI | PubMed | Europe PMC
 
[22]
2011 | Journal Article | IST-REx-ID: 9483 | OA
Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 2011;108(5):1755-1762. doi:10.1073/pnas.1019273108
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[21]
2011 | Other Publication | IST-REx-ID: 9522 | OA
Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation. Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[20]
2010 | Journal Article | IST-REx-ID: 9485 | OA
Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734. doi:10.1073/pnas.1009695107
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
2010 | Journal Article | IST-REx-ID: 9489 | OA
Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[18]
2010 | Journal Article | IST-REx-ID: 9452
Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366
View | DOI | PubMed | Europe PMC
 
[17]
2009 | Journal Article | IST-REx-ID: 9453 | OA
Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. Science. 2009;324(5933):1451-1454. doi:10.1126/science.1172417
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[16]
2008 | Journal Article | IST-REx-ID: 9537
Zilberman D. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004
View | DOI | PubMed | Europe PMC
 
[15]
2008 | Journal Article | IST-REx-ID: 9457 | OA
Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129. doi:10.1038/nature07324
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[14]
2007 | Journal Article | IST-REx-ID: 9487 | OA
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 2007;104(16):6752-6757. doi:10.1073/pnas.0701861104
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[13]
2007 | Other Publication | IST-REx-ID: 9504
Zilberman D. The Human Promoter Methylome. Vol 39. Nature Publishing Group; 2007:442-443. doi:10.1038/ng0407-442
View | DOI | PubMed | Europe PMC
 
[12]
2007 | Journal Article | IST-REx-ID: 9524 | OA
Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. Development. 2007;134(22):3959-3965. doi:10.1242/dev.001131
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
2006 | Journal Article | IST-REx-ID: 9505
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 2006;39(1):61-69. doi:10.1038/ng1929
View | DOI | PubMed | Europe PMC
 
[10]
2005 | Journal Article | IST-REx-ID: 9491 | OA
Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
2005 | Journal Article | IST-REx-ID: 9514 | OA
Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[8]
2005 | Journal Article | IST-REx-ID: 9529
Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 2005;15(5):557-562. doi:10.1016/j.gde.2005.07.002
View | DOI | PubMed | Europe PMC
 
[7]
2004 | Journal Article | IST-REx-ID: 9493 | OA
Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[6]
2004 | Journal Article | IST-REx-ID: 9517 | OA
Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
2004 | Journal Article | IST-REx-ID: 9511 | OA
Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 2004;5(12). doi:10.1186/gb-2004-5-12-249
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[4]
2004 | Journal Article | IST-REx-ID: 9454
Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336. doi:10.1126/science.1095989
View | DOI | PubMed | Europe PMC
 
[3]
2003 | Journal Article | IST-REx-ID: 9495 | OA
Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217. doi:10.1016/j.cub.2003.11.052
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[2]
2003 | Journal Article | IST-REx-ID: 9455
Zilberman D, Cao Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716-719. doi:10.1126/science.1079695
View | DOI | PubMed | Europe PMC
 
[1]
2001 | Journal Article | IST-REx-ID: 9444
Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745
View | DOI | PubMed | Europe PMC
 
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48 Publications

Mark all

[48]
2023 | Journal Article | IST-REx-ID: 12672 | OA
Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132
[Published Version] View | Files available | DOI | WoS
 
[47]
2023 | Journal Article | IST-REx-ID: 14551 | OA
Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[46]
2023 | Journal Article | IST-REx-ID: 13965 | OA
Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 2023;81(8). doi:10.1016/j.gde.2023.102087
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[45]
2021 | Journal Article | IST-REx-ID: 9877 | OA
Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[44]
2021 | Journal Article | IST-REx-ID: 10533 | OA
Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 
[43]
2020 | Journal Article | IST-REx-ID: 9526 | OA
Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. 2020;77(2):310-323.e7. doi:10.1016/j.molcel.2019.10.011
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[42]
2019 | Journal Article | IST-REx-ID: 9460 | OA
Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[41]
2019 | Journal Article | IST-REx-ID: 9530 | OA
Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[40]
2018 | Journal Article | IST-REx-ID: 9471 | OA
Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[39]
2017 | Journal Article | IST-REx-ID: 9445 | OA
Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[38]
2017 | Journal Article | IST-REx-ID: 9506 | OA
Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[37]
2016 | Journal Article | IST-REx-ID: 9456 | OA
Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[36]
2016 | Journal Article | IST-REx-ID: 9477 | OA
Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[35]
2016 | Journal Article | IST-REx-ID: 9473 | OA
Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[34]
2015 | Journal Article | IST-REx-ID: 9532 | OA
Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 
[33]
2014 | Journal Article | IST-REx-ID: 9519
Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
View | DOI | PubMed | Europe PMC
 
[32]
2014 | Journal Article | IST-REx-ID: 9458 | OA
Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[31]
2014 | Journal Article | IST-REx-ID: 9479 | OA
Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[30]
2013 | Journal Article | IST-REx-ID: 9459 | OA
Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[29]
2013 | Journal Article | IST-REx-ID: 9481 | OA
Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939. doi:10.1073/pnas.1306164110
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[28]
2013 | Journal Article | IST-REx-ID: 9520 | OA
Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[27]
2012 | Journal Article | IST-REx-ID: 9451 | OA
Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364. doi:10.1126/science.1224839
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[26]
2012 | Journal Article | IST-REx-ID: 9535 | OA
Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 2012;77:147-154. doi:10.1101/sqb.2012.77.014944
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[25]
2012 | Journal Article | IST-REx-ID: 9499 | OA
Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3). doi:10.1371/journal.pgen.1002512
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 9497 | OA
Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 2012;8(10). doi:10.1371/journal.pgen.1002988
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[23]
2012 | Journal Article | IST-REx-ID: 9528
Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007
View | DOI | PubMed | Europe PMC
 
[22]
2011 | Journal Article | IST-REx-ID: 9483 | OA
Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 2011;108(5):1755-1762. doi:10.1073/pnas.1019273108
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[21]
2011 | Other Publication | IST-REx-ID: 9522 | OA
Zilberman D. Balancing Parental Contributions in Plant Embryonic Gene Activation. Vol 20. Elsevier; 2011:735-736. doi:10.1016/j.devcel.2011.05.018
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[20]
2010 | Journal Article | IST-REx-ID: 9485 | OA
Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734. doi:10.1073/pnas.1009695107
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[19]
2010 | Journal Article | IST-REx-ID: 9489 | OA
Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[18]
2010 | Journal Article | IST-REx-ID: 9452
Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366
View | DOI | PubMed | Europe PMC
 
[17]
2009 | Journal Article | IST-REx-ID: 9453 | OA
Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. Science. 2009;324(5933):1451-1454. doi:10.1126/science.1172417
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[16]
2008 | Journal Article | IST-REx-ID: 9537
Zilberman D. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004
View | DOI | PubMed | Europe PMC
 
[15]
2008 | Journal Article | IST-REx-ID: 9457 | OA
Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129. doi:10.1038/nature07324
[Submitted Version] View | DOI | Download Submitted Version (ext.) | PubMed | Europe PMC
 
[14]
2007 | Journal Article | IST-REx-ID: 9487 | OA
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 2007;104(16):6752-6757. doi:10.1073/pnas.0701861104
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[13]
2007 | Other Publication | IST-REx-ID: 9504
Zilberman D. The Human Promoter Methylome. Vol 39. Nature Publishing Group; 2007:442-443. doi:10.1038/ng0407-442
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[12]
2007 | Journal Article | IST-REx-ID: 9524 | OA
Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. Development. 2007;134(22):3959-3965. doi:10.1242/dev.001131
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[11]
2006 | Journal Article | IST-REx-ID: 9505
Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 2006;39(1):61-69. doi:10.1038/ng1929
View | DOI | PubMed | Europe PMC
 
[10]
2005 | Journal Article | IST-REx-ID: 9491 | OA
Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[9]
2005 | Journal Article | IST-REx-ID: 9514 | OA
Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[8]
2005 | Journal Article | IST-REx-ID: 9529
Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 2005;15(5):557-562. doi:10.1016/j.gde.2005.07.002
View | DOI | PubMed | Europe PMC
 
[7]
2004 | Journal Article | IST-REx-ID: 9493 | OA
Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[6]
2004 | Journal Article | IST-REx-ID: 9517 | OA
Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[5]
2004 | Journal Article | IST-REx-ID: 9511 | OA
Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 2004;5(12). doi:10.1186/gb-2004-5-12-249
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[4]
2004 | Journal Article | IST-REx-ID: 9454
Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336. doi:10.1126/science.1095989
View | DOI | PubMed | Europe PMC
 
[3]
2003 | Journal Article | IST-REx-ID: 9495 | OA
Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217. doi:10.1016/j.cub.2003.11.052
[Published Version] View | DOI | Download Published Version (ext.) | PubMed | Europe PMC
 
[2]
2003 | Journal Article | IST-REx-ID: 9455
Zilberman D, Cao Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716-719. doi:10.1126/science.1079695
View | DOI | PubMed | Europe PMC
 
[1]
2001 | Journal Article | IST-REx-ID: 9444
Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745
View | DOI | PubMed | Europe PMC
 
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