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Daniel Zilberman - Publications

Affiliations: 
University of California, Berkeley, Berkeley, CA, United States 
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. PMID 37944515 DOI: 10.1016/j.cels.2023.10.007  0.55
2023 Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics & Development. 81: 102087. PMID 37441873 DOI: 10.1016/j.gde.2023.102087  0.494
2023 Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42: 112132. PMID 36827183 DOI: 10.1016/j.celrep.2023.112132  0.855
2021 Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in heterochromatin. Elife. 10. PMID 34850679 DOI: 10.7554/eLife.72676  0.618
2021 Rodrigues JA, Hsieh PH, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34272287 DOI: 10.1073/pnas.2104445118  0.579
2019 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. PMID 31732458 DOI: 10.1016/J.Molcel.2019.10.011  0.681
2019 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 & Chromatin. 12: 62. PMID 31601251 DOI: 10.1186/S13072-019-0307-4  0.86
2019 Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences of the United States of America. PMID 31000601 DOI: 10.1073/Pnas.1821435116  0.689
2018 Frost JM, Kim MY, Park GT, Hsieh PH, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. FACT complex is required for DNA demethylation at heterochromatin during reproduction in . Proceedings of the National Academy of Sciences of the United States of America. PMID 29712855 DOI: 10.1073/Pnas.1713333115  0.584
2018 Zilberman D, Penfield S, Feng X. Decision letter: Non-canonical RNA-directed DNA methylation participates in maternal and environmental control of seed dormancy Elife. DOI: 10.7554/Elife.37434.028  0.693
2017 Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife. 6. PMID 29140247 DOI: 10.7554/Elife.30674  0.731
2017 Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18: 87. PMID 28486944 DOI: 10.1186/S13059-017-1230-2  0.567
2017 Lyons DB, Zilberman D. Author response: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes Elife. DOI: 10.7554/Elife.30674.028  0.649
2016 Hsieh PH, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences of the United States of America. PMID 27956643 DOI: 10.1073/Pnas.1619074114  0.849
2016 Park K, Kim MY, Vickers M, Park JS, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences of the United States of America. PMID 27956642 DOI: 10.1073/Pnas.1619047114  0.764
2016 Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature. PMID 27760113 DOI: 10.1038/Nature20110  0.775
2015 Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. Genes & Development. 29: 2517-31. PMID 26680300 DOI: 10.1101/Gad.269902.115  0.535
2014 Mérai Z, Chumak N, García-Aguilar M, Hsieh TF, Nishimura T, Schoft VK, Bindics J, Slusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences of the United States of America. 111: 16166-71. PMID 25344531 DOI: 10.1073/Pnas.1418564111  0.428
2014 Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156: 1286-97. PMID 24630728 DOI: 10.1016/J.Cell.2014.01.029  0.841
2014 Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19: 320-6. PMID 24618094 DOI: 10.1016/J.Tplants.2014.01.014  0.597
2013 Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 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 of the United States of America. 110: 7934-9. PMID 23613580 DOI: 10.1073/Pnas.1306164110  0.542
2013 Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153: 193-205. PMID 23540698 DOI: 10.1016/J.Cell.2013.02.033  0.863
2013 Feng X, Zilberman D, Dickinson H. A conversation across generations: soma-germ cell crosstalk in plants. Developmental Cell. 24: 215-25. PMID 23410937 DOI: 10.1016/J.Devcel.2013.01.014  0.679
2012 Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression Cold Spring Harbor Symposia On Quantitative Biology. 77: 147-154. PMID 23250988 DOI: 10.1101/Sqb.2012.77.014944  0.677
2012 Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. Plos Genetics. 8: e1002988. PMID 23071449 DOI: 10.1371/Journal.Pgen.1002988  0.643
2012 Ibarra CA, Feng X, Schoft VK, Hsieh TF, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science (New York, N.Y.). 337: 1360-4. PMID 22984074 DOI: 10.1126/Science.1224839  0.838
2012 Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. Plos Genetics. 8: e1002512. PMID 22457632 DOI: 10.1371/Journal.Pgen.1002512  0.441
2012 Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics & Development. 22: 132-8. PMID 22336527 DOI: 10.1016/J.Gde.2012.01.007  0.801
2011 Zilberman D. Balancing parental contributions in plant embryonic gene activation. Developmental Cell. 20: 735-6. PMID 21664571 DOI: 10.1016/J.Devcel.2011.05.018  0.409
2011 Hsieh TF, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences of the United States of America. 108: 1755-62. PMID 21257907 DOI: 10.1073/Pnas.1019273108  0.578
2010 Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences of the United States of America. 107: 18729-34. PMID 20937895 DOI: 10.1073/Pnas.1009695107  0.861
2010 Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology : Cb. 20: R780-5. PMID 20833323 DOI: 10.1016/J.Cub.2010.07.007  0.85
2010 Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science (New York, N.Y.). 328: 916-9. PMID 20395474 DOI: 10.1126/Science.1186366  0.869
2009 Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science (New York, N.Y.). 324: 1451-4. PMID 19520962 DOI: 10.1126/Science.1172417  0.832
2009 Choi Y, Huh JH, Gehring M, Hsieh T, Ibarra C, Silva P, Zilberman D, Fischer RL. S05-02. Regulation of gene imprinting in arabidopsis Mechanisms of Development. 126: S6. DOI: 10.1016/J.Mod.2009.06.955  0.303
2008 Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456: 125-9. PMID 18815594 DOI: 10.1038/Nature07324  0.788
2008 Zilberman D. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11: 554-9. PMID 18774331 DOI: 10.1016/J.Pbi.2008.07.004  0.718
2007 Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. Development (Cambridge, England). 134: 3959-65. PMID 17928417 DOI: 10.1242/Dev.001131  0.778
2007 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 of the United States of America. 104: 6752-7. PMID 17409185 DOI: 10.1073/Pnas.0701861104  0.792
2007 Zilberman D. The human promoter methylome. Nature Genetics. 39: 442-3. PMID 17392803 DOI: 10.1038/Ng0407-442  0.673
2007 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. 39: 61-9. PMID 17128275 DOI: 10.1038/Ng1929  0.803
2007 Fischer R, Huh J, Penterman J, Gehring M, Zilberman D, Ballinger T, Henikoff S. DNA demethylation by the base‐excision DNA repair pathway in Arabidopsis The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A206  0.491
2005 Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6: R90. PMID 16277745 DOI: 10.1186/Gb-2005-6-11-R90  0.854
2005 Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence Current Opinion in Genetics and Development. 15: 557-562. PMID 16085410 DOI: 10.1016/J.Gde.2005.07.002  0.736
2005 Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology : Cb. 15: 154-9. PMID 15668172 DOI: 10.1016/J.Cub.2005.01.008  0.81
2004 Zilberman D, Henikoff S. Silencing of transposons in plant genomes: Kick them when they're down Genome Biology. 5. PMID 15575975 DOI: 10.1186/Gb-2004-5-12-249  0.776
2004 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 : Cb. 14: 1214-20. PMID 15242620 DOI: 10.1016/J.Cub.2004.06.055  0.76
2004 Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. Plos Biology. 2: E104. PMID 15024409 DOI: 10.1371/Journal.Pbio.0020104  0.57
2004 Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science (New York, N.Y.). 303: 1336. PMID 14988555 DOI: 10.1126/Science.1095989  0.837
2003 Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology : Cb. 13: 2212-7. PMID 14680640 DOI: 10.1016/J.Cub.2003.11.052  0.792
2003 Zilberman D, Cao X, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science (New York, N.Y.). 299: 716-9. PMID 12522258 DOI: 10.1126/Science.1079695  0.8
2001 Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation Science. 292: 2077-2080. PMID 11349138 DOI: 10.1126/Science.1059745  0.818
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