J Choi, DB Lyons, MY Kim, JD Moore, D Zilberman. (2020) DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell, 77, 1-14. PDF

JM Frost, MY Kim, GT Park, PH Hsieh, M Nakamura, SJH Lin, H Yoo, J Choi, Y Ikeda, T Kinoshita, Y Choi, D Zilberman. (2018) FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences, 115 (20), E4720-E4729. PDF

D Zilberman. (2017) An evolutionary case for functional gene body methylation in plants and animals. Genome biology, 18 (1), 87. PDF

DB Lyons, D Zilberman. (2017) DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife, 6, e30674. PDF

K Park, MY Kim, M Vickers, JS Park, Y Hyun, T Okamoto, D Zilberman, RL Fischer, X Feng, Y Choi, S Scholten. (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences, 113 (52), 15138-15143. PDF

JT Huff, D Zilberman, SW Roy. (2016) Mechanism for DNA transposons to generate introns on genomic scales. Nature, 538 (7626), 533. PDF

PH Hsieh, S He, T Buttress, H Gao, M Couchman, RL Fischer, D Zilberman, X Feng. (2016) Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences, 113 (52), 15132-15137. PDF

JA Rodrigues, D Zilberman. (2015) Evolution and function of genomic imprinting in plants. Genes & development, 29 (24), 2517-2531. PDF

MY Kim, D Zilberman. (2014) DNA methylation as a system of plant genomic immunity. Trends in plant science, 19 (5), 320-326. PDF

JT Huff, D Zilberman. (2014) Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell, 156 (6), 1286-1297. PDF

Z Mérai, N Chumak, M García-Aguilar, TF Hsieh, T Nishimura, VK Schoft, J Bindics, L Slusarz, S Arnoux, S Opravil, K Mechtler, D Zilberman, RL Fischer, H Tamaru. (2014) The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences, 111 (45), 16166-16171. PDF

A Zemach, MY Kim, PH Hsieh, D Coleman-Derr, L Eshed-Williams, K Thao, SL Harmer, D Zilberman. (2013) The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin. Cell, 153 (1), 193-205. PDF

JA Rodrigues, R Ruan, T Nishimura, MK Sharma, R Sharma, PC Ronald, RL Fischer, D Zilberman. (2013) 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, 110 (19), 7934-7939. PDF

X Feng, D Zilberman, H Dickinson. (2013) A conversation across generations: soma-germ cell crosstalk in plants. Developmental cell, 24 (3), 215-225. PDF

CA Ibarra, X Feng, VK Schoft, TF Hsieh, R Uzawa, JA Rodrigues, A Zemach, N Chumak, A Machlicova, T Nishimura, D Rojas, RL Fischer, H Tamaru, D Zilberman. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science, 337 (6100), 1360-1364. PDF

D Coleman-Derr, D Zilberman. (2012) Deposition of histone variant H2A. Z within gene bodies regulates responsive genes. PLoS genetics, 8 (10), e1002988. PDF

SY Kim, J Lee, L Eshed-Williams, D Zilberman, ZR Sung. (2012) EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS genetics, 8 (3), e1002512. PDF

D Coleman-Derr, D Zilberman. (2012) DNA methylation, H2A. Z, and the regulation of constitutive expression. Cold Spring Harbor symposia on quantitative biology, 77, 147-154. PDF

JT Huff, D Zilberman. (2012) Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current opinion in genetics & development, 22 (2), 132-138. PDF

TF Hsieh, J Shin, R Uzawa, P Silva, S Cohen, MJ Bauer, M Hashimoto, RC Kirkbride, JJ Harada, D Zilberman, RL Fischer. (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences, 108 (5), 1755-1762. PDF

D Zilberman. (2011) Balancing parental contributions in plant embryonic gene activation. Developmental cell, 20 (6), 735-736. PDF

A Zemach, IE McDaniel, P Silva, D Zilberman. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328 (5980), 916-919. PDF

A Zemach, MY Kim, P Silva, JA Rodrigues, B Dotson, MD Brooks, D Zilberman. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences, 107 (43), 18729-18734. PDF

A Zemach, D Zilberman. (2010) Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current biology, 20 (17), R780-R785. PDF

TF Hsieh, CA Ibarra, P Silva, A Zemach, L Eshed-Williams, RL Fischer, D Zilberman. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science, 324 (5933), 1451-1454. PDF

D Zilberman, D Coleman-Derr, T Ballinger, S Henikoff. (2008) Histone H2A. Z and DNA methylation are mutually antagonistic chromatin marks. Nature, 456 (7218), 125. PDF

D Zilberman. (2008) The evolving functions of DNA methylation. Current opinion in plant biology, 11 (5), 554-559. PDF

D Zilberman, M Gehring, RK Tran, T Ballinger, S Henikoff. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature genetics, 39 (1), 61. PDF

J Penterman, D Zilberman, JH Huh, T Ballinger, S Henikoff, RL Fischer. (2007) DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences, 104 (16), 6752-6757. PDF

D Zilberman, S Henikoff. (2007) Genome-wide analysis of DNA methylation patterns. Development, 134 (22), 3959-3965. PDF

D Zilberman. (2007) The human promoter methylome. Nature genetics, 39 (4), 442. PDF

RK Tran, JG Henikoff, D Zilberman, RF Ditt, SE Jacobsen, S Henikoff. (2005) DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes. Current Biology, 15 (2), 154-159. PDF

RK Tran, D Zilberman, C de Bustos, RF Ditt, JG Henikoff, AM Lindroth, J Delrow, T Boyle, S Kwong, TD Bryson, SE Jacobsen, S Henikoff. (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome biology, 6 (11), R90. PDF

D Zilberman, S Henikoff. (2005) Epigenetic inheritance in Arabidopsis: selective silence. Current opinion in genetics & development, 15 (5), 557-562. PDF

Z Xie, LK Johansen, AM Gustafson, KD Kasschau, AD Lellis, D Zilberman, SE Jacobsen, JC Carrington. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS biology, 2 (5), e104. PDF

SWL Chan, D Zilberman, Z Xie, LK Johansen, JC Carrington, SE Jacobsen. (2004) RNA silencing genes control de novo DNA methylation. Science, 303 (5662), 1336-1336. PDF

D Zilberman, X Cao, LK Johansen, Z Xie, JC Carrington, SE Jacobsen. (2004) Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats. Current Biology, 14 (13), 1214-1220. PDF

D Zilberman, S Henikoff. (2004) Silencing of transposons in plant genomes: kick them when they’re down. Genome biology, 5 (12), 249. PDF

D Zilberman. (2004) RNA-directed chromatin modification in Arabidopsis thaliana. PhD Thesis.

D Zilberman, X Cao, SE Jacobsen. (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299 (5607), 716-719. PDF

X Cao, W Aufsatz, D Zilberman, MF Mette, MS Huang, M Matzke, SE Jacobsen. (2003) Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation. Current biology, 13 (24), 2212-2217. PDF

AM Lindroth, X Cao, JP Jackson, D Zilberman, CM McCallum, S Henikoff, SE Jacobsen. (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science, 292 (5524), 2077-2080. PDF