Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.”https://doi.org/10.1016/j.celrep.2023.112132__Cell Reports. Elsevier, 2023.https://doi.org/10.1016/j.celrep.2023.112132 .

Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.”https://doi.org/10.1016/j.cels.2023.10.007__Cell Systems. Elsevier, 2023.https://doi.org/10.1016/j.cels.2023.10.007 .

Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.”https://doi.org/10.1016/j.gde.2023.102087__Current Opinion in Genetics and Development. Elsevier, 2023.https://doi.org/10.1016/j.gde.2023.102087 .

Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.”https://doi.org/10.1073/pnas.2104445118__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021.https://doi.org/10.1073/pnas.2104445118 .

Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histonehttps://doi.org/10.7554/elife.72676__Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.”https://doi.org/10.7554/elife.72676__ELife. eLife Sciences Publications, 2021.https://doi.org/10.7554/elife.72676 .

Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel Zilberman. “DNA Methylation and Histonehttps://doi.org/10.1016/j.molcel.2019.10.011__Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.”https://doi.org/10.1016/j.molcel.2019.10.011__Molecular Cell. Elsevier, 2020.https://doi.org/10.1016/j.molcel.2019.10.011 .

Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROa in Rice Vegetative Cells Promotes Methylation in Sperm.”https://doi.org/10.1073/pnas.1821435116__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019.https://doi.org/10.1073/pnas.1821435116 .

Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.”https://doi.org/10.1186/s13072-019-0307-4__Epigenetics and Chromatin. Springer Nature, 2019.https://doi.org/10.1186/s13072-019-0307-4 .

Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.”https://doi.org/10.1073/pnas.1713333115__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018.https://doi.org/10.1073/pnas.1713333115 .

Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.”https://doi.org/10.7554/elife.30674__ELife. eLife Sciences Publications, 2017.https://doi.org/10.7554/elife.30674 .

Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.”https://doi.org/10.1186/s13059-017-1230-2__Genome Biology. Springer Nature, 2017.https://doi.org/10.1186/s13059-017-1230-2 .

Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.”https://doi.org/10.1038/nature20110__Nature. Springer Nature , 2016.https://doi.org/10.1038/nature20110 .

Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.”https://doi.org/10.1073/pnas.1619047114__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016.https://doi.org/10.1073/pnas.1619047114 .

Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”https://doi.org/10.1073/pnas.1619074114__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016.https://doi.org/10.1073/pnas.1619074114 .

Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.”https://doi.org/10.1101/gad.269902.115__Genes and Development. Cold Spring Harbor Laboratory Press, 2015.https://doi.org/10.1101/gad.269902.115 .

Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.”https://doi.org/10.1016/j.tplants.2014.01.014__Trends in Plant Science. Elsevier, 2014.https://doi.org/10.1016/j.tplants.2014.01.014 .

Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.”https://doi.org/10.1016/j.cell.2014.01.029__Cell. Elsevier, 2014.https://doi.org/10.1016/j.cell.2014.01.029 .

Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cd/ Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.”https://doi.org/10.1073/pnas.1418564111__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014.https://doi.org/10.1073/pnas.1418564111 .

Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access -Containing Heterochromatin.”https://doi.org/10.1016/j.cell.2013.02.033__Cell. Elsevier, 2013.https://doi.org/10.1016/j.cell.2013.02.033 .

Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”https://doi.org/10.1073/pnas.1306164110__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2013.https://doi.org/10.1073/pnas.1306164110 .

Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.”https://doi.org/10.1016/j.devcel.2013.01.014__Developmental Cell. Elsevier, 2013.https://doi.org/10.1016/j.devcel.2013.01.014 .

Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.”https://doi.org/10.1126/science.1224839__Science. American Association for the Advancement of Science, 2012.https://doi.org/10.1126/science.1224839 .

Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, A.Z, and the Regulation of Constitutive Expression.”https://doi.org/10.1101/sqb.2012.77.014944__Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press, 2012.https://doi.org/10.1101/sqb.2012.77.014944 .

Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EM and PR Cooperate to Repress Key Regulators of Arabidopsis Development.”https://doi.org/10.1371/journal.pgen.1002512__PLoS Genetics. Public Library of Science, 2012.https://doi.org/10.1371/journal.pgen.1002512 .

Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant A.Z within Gene Bodies Regulates Responsive Genes.”https://doi.org/10.1371/journal.pgen.1002988__PLoS Genetics. Public Library of Science, 2012.https://doi.org/10.1371/journal.pgen.1002988 .

Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.”https://doi.org/10.1016/j.gde.2012.01.007__Current Opinion in Genetics and Development. Elsevier, 2012.https://doi.org/10.1016/j.gde.2012.01.007 .

Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.”https://doi.org/10.1073/pnas.1019273108__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011.https://doi.org/10.1073/pnas.1019273108 .

Zilberman, Daniel. Balancing Parental Contributions in Plant Embryonic Gene Activation. Developmental Cell. Vol. 20. Elsevier, 2011.https://doi.org/10.1016/j.devcel.2011.05.018 .

Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”https://doi.org/10.1073/pnas.1009695107__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2010.https://doi.org/10.1073/pnas.1009695107 .

Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.”https://doi.org/10.1016/j.cub.2010.07.007__Current Biology. Elsevier, 2010.https://doi.org/10.1016/j.cub.2010.07.007 .

Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.”https://doi.org/10.1126/science.1186366__Science. American Association for the Advancement of Science, 2010.https://doi.org/10.1126/science.1186366 .

Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.”https://doi.org/10.1126/science.1172417__Science. American Association for the Advancement of Science, 2009.https://doi.org/10.1126/science.1172417 .

Zilberman, Daniel. “The Evolving Functions of DNA Methylation.”https://doi.org/10.1016/j.pbi.2008.07.004__Current Opinion in Plant Biology. Elsevier , 2008.https://doi.org/10.1016/j.pbi.2008.07.004 .

Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”https://doi.org/10.1038/nature07324__Nature. Springer Nature, 2008.https://doi.org/10.1038/nature07324 .

Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.”https://doi.org/10.1073/pnas.0701861104__Proceedings of the National Academy of Sciences. National Academy of Sciences, 2007.https://doi.org/10.1073/pnas.0701861104 .

Zilberman, Daniel. The Human Promoter Methylome. Nature Genetics. Vol. 39. Nature Publishing Group, 2007.https://doi.org/10.1038/ng0407-442 .

Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.”https://doi.org/10.1242/dev.001131__Development. The Company of Biologists, 2007.https://doi.org/10.1242/dev.001131 .

Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.”https://doi.org/10.1038/ng1929__Nature Genetics. Nature Publishing Group, 2006.https://doi.org/10.1038/ng1929 .

Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.”https://doi.org/10.1016/j.cub.2005.01.008__Current Biology. Elsevier, 2005.https://doi.org/10.1016/j.cub.2005.01.008 .

Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.”https://doi.org/10.1186/gb-2005-6-11-r90__Genome Biology. Springer Nature, 2005.https://doi.org/10.1186/gb-2005-6-11-r90 .

Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.”https://doi.org/10.1016/j.gde.2005.07.002__Current Opinion in Genetics and Development. Elsevier, 2005.https://doi.org/10.1016/j.gde.2005.07.002 .

Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUT in RNA-Directed DNA Methylation Triggered by Inverted Repeats.”https://doi.org/10.1016/j.cub.2004.06.055__Current Biology. Elsevier, 2004.https://doi.org/10.1016/j.cub.2004.06.055 .

Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D.https://doi.org/10.1371/journal.pbio.0020104__Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.”https://doi.org/10.1371/journal.pbio.0020104__PLoS Biology. Public Library of Science, 2004.https://doi.org/10.1371/journal.pbio.0020104 .

Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.”https://doi.org/10.1186/gb-2004-5-12-249__Genome Biology. Springer Nature, 2004.https://doi.org/10.1186/gb-2004-5-12-249 .

Chan, Simon W.-L., Daniel Zilberman,https://doi.org/10.1126/science.1095989__Zhixin Xie,https://doi.org/10.1126/science.1095989__Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.”https://doi.org/10.1126/science.1095989__Science. American Association for the Advancement of Science, 2004.https://doi.org/10.1126/science.1095989 .

Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CM Methyltransferases in RNA-Directed DNA Methylation.”https://doi.org/10.1016/j.cub.2003.11.052__Current Biology. Elsevier, 2003.https://doi.org/10.1016/j.cub.2003.11.052 .

Zilberman, Daniel,https://doi.org/10.1126/science.1079695__Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUT Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.”https://doi.org/10.1126/science.1079695__Science. American Association for the Advancement of Science, 2003.https://doi.org/10.1126/science.1079695 .

Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLAS for Maintenance of CpXpG Methylation.”https://doi.org/10.1126/science.1059745__Science. American Association for the Advancement of Science, 2001.https://doi.org/10.1126/science.1059745 .