Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J.,https://doi.org/10.1016/j.celrep.2023.112132__Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. Elsevier.https://doi.org/10.1016/j.celrep.2023.112132 
LibreCat: https://research-explorer.ista.ac.at/record/12672
DOI: 10.1016/j.celrep.2023.112132
WoS: 000944921600001

Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., &; Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier.https://doi.org/10.1016/j.cels.2023.10.007 
LibreCat: https://research-explorer.ista.ac.at/record/14551
DOI: 10.1016/j.cels.2023.10.007
PMID: 37944515

Hollwey, E., Briffa, A., Howard, M., &; Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. Elsevier.https://doi.org/10.1016/j.gde.2023.102087 
LibreCat: https://research-explorer.ista.ac.at/record/13965
DOI: 10.1016/j.gde.2023.102087
WoS: 001047020200001
PMID: 37441873

Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R.,https://doi.org/10.1073/pnas.2104445118__Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.2104445118 
LibreCat: https://research-explorer.ista.ac.at/record/9877
DOI: 10.1073/pnas.2104445118
WoS: 000685037700012
PMID: 34272287

Choi, J., Lyons, D. B., &; Zilberman, D. (2021). Histonehttps://doi.org/10.7554/elife.72676__prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications.https://doi.org/10.7554/elife.72676 
LibreCat: https://research-explorer.ista.ac.at/record/10533
DOI: 10.7554/elife.72676
WoS: 000754832000001
PMID: 34850679

Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., &; Zilberman, D. (2020). DNA methylation and histonehttps://doi.org/10.1016/j.molcel.2019.10.011__jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. Elsevier.https://doi.org/10.1016/j.molcel.2019.10.011 
LibreCat: https://research-explorer.ista.ac.at/record/9526
DOI: 10.1016/j.molcel.2019.10.011
PMID: 31732458

Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &; Fischer, R. L. (2019). DNA demethylation by ROa in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1821435116 
LibreCat: https://research-explorer.ista.ac.at/record/9460
DOI: 10.1073/pnas.1821435116
PMID: 31000601

Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature.https://doi.org/10.1186/s13072-019-0307-4 
LibreCat: https://research-explorer.ista.ac.at/record/9530
DOI: 10.1186/s13072-019-0307-4
PMID: 31601251

Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H.,https://doi.org/10.1073/pnas.1713333115__Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1713333115 
LibreCat: https://research-explorer.ista.ac.at/record/9471
DOI: 10.1073/pnas.1713333115
PMID: 29712855

Lyons, D. B., &; Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications.https://doi.org/10.7554/elife.30674 
LibreCat: https://research-explorer.ista.ac.at/record/9445
DOI: 10.7554/elife.30674
PMID: 29140247

Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature.https://doi.org/10.1186/s13059-017-1230-2 
LibreCat: https://research-explorer.ista.ac.at/record/9506
DOI: 10.1186/s13059-017-1230-2
PMID: 28486944

Huff, J. T., Zilberman, D., &; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. Nature. Springer Nature .https://doi.org/10.1038/nature20110 
LibreCat: https://research-explorer.ista.ac.at/record/9456
DOI: 10.1038/nature20110
PMID: 27760113

Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T.,https://doi.org/10.1073/pnas.1619047114__Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1619047114 
LibreCat: https://research-explorer.ista.ac.at/record/9477
DOI: 10.1073/pnas.1619047114
PMID: 27956642

Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,https://doi.org/10.1073/pnas.1619074114__Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1619074114 
LibreCat: https://research-explorer.ista.ac.at/record/9473
DOI: 10.1073/pnas.1619074114
PMID: 27956643

Rodrigues, J. A., &; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory Press.https://doi.org/10.1101/gad.269902.115 
LibreCat: https://research-explorer.ista.ac.at/record/9532
DOI: 10.1101/gad.269902.115
PMID: 26680300

Kim, M. Y., &; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. Trends in Plant Science. Elsevier.https://doi.org/10.1016/j.tplants.2014.01.014 
LibreCat: https://research-explorer.ista.ac.at/record/9519
DOI: 10.1016/j.tplants.2014.01.014
PMID: 24618094 

Huff, J. T., &; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier.https://doi.org/10.1016/j.cell.2014.01.029 
LibreCat: https://research-explorer.ista.ac.at/record/9458
DOI: 10.1016/j.cell.2014.01.029
PMID: 24630728

Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K.,https://doi.org/10.1073/pnas.1418564111__Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cd/ disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1418564111 
LibreCat: https://research-explorer.ista.ac.at/record/9479
DOI: 10.1073/pnas.1418564111
PMID: 25344531

Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K.,https://doi.org/10.1016/j.cell.2013.02.033__Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access -containing heterochromatin. Cell. Elsevier.https://doi.org/10.1016/j.cell.2013.02.033 
LibreCat: https://research-explorer.ista.ac.at/record/9459
DOI: 10.1016/j.cell.2013.02.033
PMID: 23540698

Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C.,https://doi.org/10.1073/pnas.1306164110__Zilberman, D. (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. National Academy of Sciences.https://doi.org/10.1073/pnas.1306164110 
LibreCat: https://research-explorer.ista.ac.at/record/9481
DOI: 10.1073/pnas.1306164110
PMID: 23613580

Feng, X., Zilberman, D., &; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.https://doi.org/10.1016/j.devcel.2013.01.014 
LibreCat: https://research-explorer.ista.ac.at/record/9520
DOI: 10.1016/j.devcel.2013.01.014
PMID: 23410937

Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A.,https://doi.org/10.1126/science.1224839__Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.1224839 
LibreCat: https://research-explorer.ista.ac.at/record/9451
DOI: 10.1126/science.1224839
PMID: 22984074

Coleman-Derr, D., &; Zilberman, D. (2012). DNA methylation, A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. Cold Spring Harbor Laboratory Press.https://doi.org/10.1101/sqb.2012.77.014944 
LibreCat: https://research-explorer.ista.ac.at/record/9535
DOI: 10.1101/sqb.2012.77.014944
PMID: 23250988

Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., &; Sung, Z. R. (2012). EM and PR cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1002512 
LibreCat: https://research-explorer.ista.ac.at/record/9499
DOI: 10.1371/journal.pgen.1002512
PMID: 22457632

Coleman-Derr, D., &; Zilberman, D. (2012). Deposition of histone variant A.Z within gene bodies regulates responsive genes. PLoS Genetics. Public Library of Science.https://doi.org/10.1371/journal.pgen.1002988 
LibreCat: https://research-explorer.ista.ac.at/record/9497
DOI: 10.1371/journal.pgen.1002988
PMID: 23071449

Huff, J. T., &; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. Elsevier.https://doi.org/10.1016/j.gde.2012.01.007 
LibreCat: https://research-explorer.ista.ac.at/record/9528
DOI: 10.1016/j.gde.2012.01.007
PMID: 22336527

Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J.,https://doi.org/10.1073/pnas.1019273108__Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1019273108 
LibreCat: https://research-explorer.ista.ac.at/record/9483
DOI: 10.1073/pnas.1019273108
PMID: 21257907

Zilberman, D. (2011). Balancing parental contributions in plant embryonic gene activation. Developmental Cell (Vol. 20, pp. 735–736). Elsevier.https://doi.org/10.1016/j.devcel.2011.05.018 
LibreCat: https://research-explorer.ista.ac.at/record/9522
DOI: 10.1016/j.devcel.2011.05.018
PMID: 21664571

Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.1009695107 
LibreCat: https://research-explorer.ista.ac.at/record/9485
DOI: 10.1073/pnas.1009695107
PMID: 20937895

Zemach, A., &; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. Elsevier.https://doi.org/10.1016/j.cub.2010.07.007 
LibreCat: https://research-explorer.ista.ac.at/record/9489
DOI: 10.1016/j.cub.2010.07.007
PMID: 20833323

Zemach, A., McDaniel, I. E., Silva, P., &; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.1186366 
LibreCat: https://research-explorer.ista.ac.at/record/9452
DOI: 10.1126/science.1186366
PMID: 20395474 

Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R. L., &; Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.1172417 
LibreCat: https://research-explorer.ista.ac.at/record/9453
DOI: 10.1126/science.1172417
PMID: 19520962

Zilberman, D. (2008). The evolving functions of DNA methylation. Current Opinion in Plant Biology. Elsevier .https://doi.org/10.1016/j.pbi.2008.07.004 
LibreCat: https://research-explorer.ista.ac.at/record/9537
DOI: 10.1016/j.pbi.2008.07.004
PMID: 18774331

Zilberman, D., Coleman-Derr, D., Ballinger, T., &; Henikoff, S. (2008). Histone A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. Springer Nature.https://doi.org/10.1038/nature07324 
LibreCat: https://research-explorer.ista.ac.at/record/9457
DOI: 10.1038/nature07324
PMID: 18815594

Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &; Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. National Academy of Sciences.https://doi.org/10.1073/pnas.0701861104 
LibreCat: https://research-explorer.ista.ac.at/record/9487
DOI: 10.1073/pnas.0701861104
PMID: 17409185

Zilberman, D. (2007). The human promoter methylome. Nature Genetics (Vol. 39, pp. 442–443). Nature Publishing Group.https://doi.org/10.1038/ng0407-442 
LibreCat: https://research-explorer.ista.ac.at/record/9504
DOI: 10.1038/ng0407-442
PMID: 17392803

Zilberman, D., &; Henikoff, S. (2007). Genome-wide analysis of DNA methylation patterns. Development. The Company of Biologists.https://doi.org/10.1242/dev.001131 
LibreCat: https://research-explorer.ista.ac.at/record/9524
DOI: 10.1242/dev.001131
PMID: 17928417

Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &; Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. Nature Publishing Group.https://doi.org/10.1038/ng1929 
LibreCat: https://research-explorer.ista.ac.at/record/9505
DOI: 10.1038/ng1929
PMID: 17128275

Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., &; Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. Elsevier.https://doi.org/10.1016/j.cub.2005.01.008 
LibreCat: https://research-explorer.ista.ac.at/record/9491
DOI: 10.1016/j.cub.2005.01.008
PMID: 15668172 

Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M.,https://doi.org/10.1186/gb-2005-6-11-r90__Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. Springer Nature.https://doi.org/10.1186/gb-2005-6-11-r90 
LibreCat: https://research-explorer.ista.ac.at/record/9514
DOI: 10.1186/gb-2005-6-11-r90
PMID: 16277745

Zilberman, D., &; Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. Elsevier.https://doi.org/10.1016/j.gde.2005.07.002 
LibreCat: https://research-explorer.ista.ac.at/record/9529
DOI: 10.1016/j.gde.2005.07.002
PMID: 16085410

Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &; Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUT in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. Elsevier.https://doi.org/10.1016/j.cub.2004.06.055 
LibreCat: https://research-explorer.ista.ac.at/record/9493
DOI: 10.1016/j.cub.2004.06.055
PMID: 15242620 

Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D.,https://doi.org/10.1371/journal.pbio.0020104__Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. Public Library of Science.https://doi.org/10.1371/journal.pbio.0020104 
LibreCat: https://research-explorer.ista.ac.at/record/9517
DOI: 10.1371/journal.pbio.0020104
PMID: 15024409

Zilberman, D., &; Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. Springer Nature.https://doi.org/10.1186/gb-2004-5-12-249 
LibreCat: https://research-explorer.ista.ac.at/record/9511
DOI: 10.1186/gb-2004-5-12-249
PMID: 15575975

Chan, S. W.-L., Zilberman, D., Xie,https://doi.org/10.1126/science.1095989__Zhixin, Johansen,https://doi.org/10.1126/science.1095989__Lisa K., Carrington, J. C., &; Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.1095989 
LibreCat: https://research-explorer.ista.ac.at/record/9454
DOI: 10.1126/science.1095989
PMID: 14988555

Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M., &; Jacobsen, S. E. (2003). Role of the DRM and CM methyltransferases in RNA-directed DNA methylation. Current Biology. Elsevier.https://doi.org/10.1016/j.cub.2003.11.052 
LibreCat: https://research-explorer.ista.ac.at/record/9495
DOI: 10.1016/j.cub.2003.11.052
PMID: 14680640

Zilberman, D., Cao,https://doi.org/10.1126/science.1079695__Xiaofeng, &; Jacobsen, S. E. (2003). ARGONAUT control of locus-specific siRNA accumulation and DNA and histone methylation. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.1079695 
LibreCat: https://research-explorer.ista.ac.at/record/9455
DOI: 10.1126/science.1079695
PMID: 12522258

Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff, S., &; Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLAS for maintenance of CpXpG methylation. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.1059745 
LibreCat: https://research-explorer.ista.ac.at/record/9444
DOI: 10.1126/science.1059745
PMID: 11349138