[{"year":"2013","month":"03","page":"193-205","_id":"9459","citation":{"chicago":"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 H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205."},"date_updated":"2021-12-14T08:25:35Z","publisher":"Elsevier","language":[{"iso":"eng"}],"title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","author":[{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"last_name":"Hsieh","first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung"},{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"full_name":"Eshed-Williams, Leor","first_name":"Leor","last_name":"Eshed-Williams"},{"full_name":"Thao, Ka","first_name":"Ka","last_name":"Thao"},{"first_name":"Stacey L.","last_name":"Harmer","full_name":"Harmer, Stacey L."},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"type":"journal_article","date_published":"2013-03-28T00:00:00Z","publication":"Cell","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"quality_controlled":"1","article_processing_charge":"No","issue":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.02.033"}],"extern":"1","oa":1,"status":"public","publication_status":"published","day":"28","doi":"10.1016/j.cell.2013.02.033","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.","lang":"eng"}],"volume":153,"date_created":"2021-06-04T12:23:28Z","article_type":"original","external_id":{"pmid":["23540698"]},"scopus_import":"1","intvolume":"       153"},{"extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"keyword":["Multidisciplinary"],"issue":"19","day":"07","doi":"10.1073/pnas.1306164110","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication_status":"published","abstract":[{"text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants.","lang":"eng"}],"date_created":"2021-06-07T07:31:02Z","volume":110,"article_type":"original","pmid":1,"oa_version":"Published Version","intvolume":"       110","external_id":{"pmid":["23613580"]},"scopus_import":"1","year":"2013","month":"05","_id":"9481","date_updated":"2021-12-14T08:26:44Z","citation":{"ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","ama":"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. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, 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. 110(19), 7934–7939.","apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","chicago":"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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>."},"page":"7934-7939","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2013-05-07T00:00:00Z","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"first_name":"Randy","last_name":"Ruan","full_name":"Ruan, Randy"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Sharma","first_name":"Manoj K.","full_name":"Sharma, Manoj K."},{"full_name":"Sharma, Rita","last_name":"Sharma","first_name":"Rita"},{"full_name":"Ronald, Pamela C","first_name":"Pamela C","last_name":"Ronald"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences"},{"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes.","lang":"eng"}],"date_created":"2021-06-08T06:14:50Z","volume":24,"article_type":"review","external_id":{"pmid":["23410937"]},"scopus_import":"1","intvolume":"        24","issue":"3","extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2013.01.014"}],"status":"public","publication_status":"published","day":"11","doi":"10.1016/j.devcel.2013.01.014","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A conversation across generations: Soma-germ cell crosstalk in plants","author":[{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Dickinson, Hugh","last_name":"Dickinson","first_name":"Hugh"}],"type":"journal_article","date_published":"2013-02-11T00:00:00Z","publication":"Developmental Cell","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"quality_controlled":"1","article_processing_charge":"No","year":"2013","month":"02","citation":{"chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>.","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225."},"_id":"9520","date_updated":"2023-05-08T11:00:59Z","page":"215-225","publisher":"Elsevier","language":[{"iso":"eng"}]},{"issue":"6100","extern":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"oa":1,"status":"public","publication_status":"published","day":"14","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1126/science.1224839","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations."}],"article_type":"original","date_created":"2021-06-04T07:51:31Z","volume":337,"external_id":{"pmid":["22984074"]},"scopus_import":"1","intvolume":"       337","year":"2012","_id":"9451","page":"1360-1364","citation":{"chicago":"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.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>."},"date_updated":"2021-12-14T08:28:51Z","month":"09","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","author":[{"last_name":"Ibarra","first_name":"Christian A.","full_name":"Ibarra, Christian A."},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Schoft, Vera K.","last_name":"Schoft","first_name":"Vera K."},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"first_name":"Rie","last_name":"Uzawa","full_name":"Uzawa, Rie"},{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"first_name":"Nina","last_name":"Chumak","full_name":"Chumak, Nina"},{"first_name":"Adriana","last_name":"Machlicova","full_name":"Machlicova, Adriana"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"first_name":"Denisse","last_name":"Rojas","full_name":"Rojas, Denisse"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"full_name":"Tamaru, Hisashi","first_name":"Hisashi","last_name":"Tamaru"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel"}],"title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","type":"journal_article","has_accepted_license":"1","date_published":"2012-09-14T00:00:00Z","ddc":["580"],"publication":"Science","quality_controlled":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_processing_charge":"No"},{"year":"2012","language":[{"iso":"eng"}],"publisher":"Public Library of Science","_id":"9497","citation":{"ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” <i>PLoS Genetics</i>, vol. 8, no. 10. Public Library of Science, 2012.","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. 2012;8(10). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>.","chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>."},"date_updated":"2021-12-14T08:29:57Z","month":"10","date_published":"2012-10-11T00:00:00Z","type":"journal_article","author":[{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"publication":"PLoS Genetics","extern":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"issue":"10","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1371/journal.pgen.1002988","day":"11","publication_status":"published","status":"public","article_type":"original","volume":8,"date_created":"2021-06-07T10:55:27Z","abstract":[{"lang":"eng","text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes."}],"article_number":"e1002988","oa_version":"Published Version","pmid":1,"intvolume":"         8","scopus_import":"1","external_id":{"pmid":["23071449"]}},{"year":"2012","language":[{"iso":"eng"}],"publisher":"Public Library of Science","_id":"9499","date_updated":"2021-12-14T08:31:14Z","citation":{"mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>.","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. 2012;8(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” <i>PLoS Genetics</i>, vol. 8, no. 3. Public Library of Science, 2012.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., &#38; Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>","ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>."},"month":"03","author":[{"full_name":"Kim, Sang Yeol","last_name":"Kim","first_name":"Sang Yeol"},{"full_name":"Lee, Jungeun","first_name":"Jungeun","last_name":"Lee"},{"first_name":"Leor","last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Z. Renee","last_name":"Sung","full_name":"Sung, Z. Renee"}],"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","date_published":"2012-03-22T00:00:00Z","type":"journal_article","publication":"PLoS Genetics","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"issue":"3","oa":1,"extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"publication_status":"published","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1371/journal.pgen.1002512","day":"22","oa_version":"Published Version","pmid":1,"article_type":"original","date_created":"2021-06-07T11:07:56Z","volume":8,"abstract":[{"lang":"eng","text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism."}],"article_number":"e1002512","scopus_import":"1","external_id":{"pmid":["22457632"]},"intvolume":"         8"},{"title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"type":"journal_article","date_published":"2012-04-01T00:00:00Z","publication":"Current Opinion in Genetics and Development","publication_identifier":{"issn":["0959-437X"]},"quality_controlled":"1","article_processing_charge":"No","year":"2012","month":"04","date_updated":"2021-12-14T08:32:38Z","_id":"9528","citation":{"short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","apa":"Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. 2012;22(2):132-138. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>."},"page":"132-138","publisher":"Elsevier","language":[{"iso":"eng"}],"pmid":1,"oa_version":"None","abstract":[{"text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory.","lang":"eng"}],"date_created":"2021-06-08T08:58:52Z","volume":22,"article_type":"review","external_id":{"pmid":["22336527"]},"scopus_import":"1","intvolume":"        22","issue":"2","extern":"1","status":"public","publication_status":"published","doi":"10.1016/j.gde.2012.01.007","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"extern":"1","oa":1,"day":"18","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1101/sqb.2012.77.014944","status":"public","publication_status":"published","abstract":[{"text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies.","lang":"eng"}],"article_type":"review","date_created":"2021-06-08T13:01:23Z","volume":77,"oa_version":"Published Version","pmid":1,"intvolume":"        77","external_id":{"pmid":["23250988"]},"scopus_import":"1","year":"2012","page":"147-154","_id":"9535","citation":{"chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2012. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>.","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2012;77:147-154. doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>"},"date_updated":"2021-12-14T08:33:09Z","month":"12","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory Press","type":"journal_article","date_published":"2012-12-18T00:00:00Z","author":[{"first_name":"D.","last_name":"Coleman-Derr","full_name":"Coleman-Derr, D."},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","quality_controlled":"1","publication_identifier":{"issn":["0091-7451"],"eissn":["1943-4456"]},"article_processing_charge":"No","publication":"Cold Spring Harbor Symposia on Quantitative Biology"},{"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","_id":"9483","citation":{"chicago":"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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>.","short":"T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762.","apa":"Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>","ista":"Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762.","ama":"Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(5):1755-1762. doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>","mla":"Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>.","ieee":"T.-F. Hsieh <i>et al.</i>, “Regulation of imprinted gene expression in Arabidopsis endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011."},"page":"1755-1762","date_updated":"2021-12-14T08:33:49Z","month":"02","year":"2011","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","date_published":"2011-02-01T00:00:00Z","type":"journal_article","author":[{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"full_name":"Shin, Juhyun","last_name":"Shin","first_name":"Juhyun"},{"full_name":"Uzawa, Rie","last_name":"Uzawa","first_name":"Rie"},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"last_name":"Cohen","first_name":"Stephanie","full_name":"Cohen, Stephanie"},{"first_name":"Matthew J.","last_name":"Bauer","full_name":"Bauer, Matthew J."},{"first_name":"Meryl","last_name":"Hashimoto","full_name":"Hashimoto, Meryl"},{"full_name":"Kirkbride, Ryan C.","last_name":"Kirkbride","first_name":"Ryan C."},{"full_name":"Harada, John J.","first_name":"John J.","last_name":"Harada"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"title":"Regulation of imprinted gene expression in Arabidopsis endosperm","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1073/pnas.1019273108","day":"01","publication_status":"published","status":"public","oa":1,"extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1019273108"}],"issue":"5","intvolume":"       108","scopus_import":"1","external_id":{"pmid":["21257907"]},"article_type":"original","volume":108,"date_created":"2021-06-07T07:40:38Z","abstract":[{"lang":"eng","text":"Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development."}],"oa_version":"Published Version","pmid":1},{"day":"14","doi":"10.1016/j.devcel.2011.05.018","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"status":"public","publication_status":"published","extern":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2011.05.018","open_access":"1"}],"issue":"6","intvolume":"        20","external_id":{"pmid":["21664571"]},"abstract":[{"lang":"eng","text":"Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo."}],"volume":20,"date_created":"2021-06-08T06:23:39Z","pmid":1,"oa_version":"Published Version","month":"06","citation":{"ista":"Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p.","short":"D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011.","apa":"Zilberman, D. (2011). <i>Balancing parental contributions in plant embryonic gene activation</i>. <i>Developmental Cell</i> (Vol. 20, pp. 735–736). Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">https://doi.org/10.1016/j.devcel.2011.05.018</a>","ieee":"D. Zilberman, <i>Balancing parental contributions in plant embryonic gene activation</i>, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.","mla":"Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” <i>Developmental Cell</i>, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">10.1016/j.devcel.2011.05.018</a>.","ama":"Zilberman D. <i>Balancing Parental Contributions in Plant Embryonic Gene Activation</i>. Vol 20. Elsevier; 2011:735-736. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">10.1016/j.devcel.2011.05.018</a>","chicago":"Zilberman, Daniel. <i>Balancing Parental Contributions in Plant Embryonic Gene Activation</i>. <i>Developmental Cell</i>. Vol. 20. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">https://doi.org/10.1016/j.devcel.2011.05.018</a>."},"_id":"9522","date_updated":"2021-12-14T08:34:37Z","page":"735-736","publisher":"Elsevier","language":[{"iso":"eng"}],"year":"2011","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Developmental Cell","type":"other_academic_publication","date_published":"2011-06-14T00:00:00Z","title":"Balancing parental contributions in plant embryonic gene activation","author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"}]},{"date_published":"2010-05-14T00:00:00Z","type":"journal_article","author":[{"full_name":"Zemach, Assaf ","last_name":"Zemach","first_name":"Assaf "},{"last_name":"McDaniel","first_name":"Ivy E.","full_name":"McDaniel, Ivy E."},{"last_name":"Silva","first_name":"Pedro","full_name":"Silva, Pedro"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication":"Science","year":"2010","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","date_updated":"2021-12-14T08:35:37Z","_id":"9452","citation":{"chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>.","ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010."},"page":"916-919","month":"05","article_type":"original","volume":328,"date_created":"2021-06-04T08:26:08Z","abstract":[{"text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.","lang":"eng"}],"oa_version":"None","pmid":1,"intvolume":"       328","scopus_import":"1","external_id":{"pmid":["20395474 "]},"keyword":["Multidisciplinary"],"extern":"1","issue":"5980","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1126/science.1186366","day":"14","publication_status":"published","status":"public"},{"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","_id":"9485","date_updated":"2021-12-14T08:40:02Z","citation":{"apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","chicago":"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.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>."},"page":"18729-18734","month":"10","year":"2010","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","date_published":"2010-10-26T00:00:00Z","type":"journal_article","author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"last_name":"Dotson","first_name":"Bradley","full_name":"Dotson, Bradley"},{"last_name":"Brooks","first_name":"Matthew D.","full_name":"Brooks, Matthew D."},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"title":"Local DNA hypomethylation activates genes in rice endosperm","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1073/pnas.1009695107","day":"26","publication_status":"published","status":"public","extern":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"oa":1,"issue":"43","intvolume":"       107","scopus_import":"1","external_id":{"pmid":["20937895"]},"article_type":"original","volume":107,"date_created":"2021-06-07T09:31:01Z","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"oa_version":"Published Version","pmid":1},{"issue":"17","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"extern":"1","oa":1,"publication_status":"published","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1016/j.cub.2010.07.007","day":"14","oa_version":"Published Version","pmid":1,"article_type":"review","volume":20,"date_created":"2021-06-07T09:45:27Z","abstract":[{"text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.","lang":"eng"}],"scopus_import":"1","external_id":{"pmid":["20833323"]},"intvolume":"        20","year":"2010","language":[{"iso":"eng"}],"publisher":"Elsevier","_id":"9489","citation":{"chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>."},"page":"R780-R785","date_updated":"2021-12-14T08:52:34Z","month":"09","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","date_published":"2010-09-14T00:00:00Z","type":"journal_article","publication":"Current Biology","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]}},{"_id":"9453","citation":{"chicago":"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.” <i>Science</i>. American Association for the Advancement of Science, 2009. <a href=\"https://doi.org/10.1126/science.1172417\">https://doi.org/10.1126/science.1172417</a>.","mla":"Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.” <i>Science</i>, vol. 324, no. 5933, American Association for the Advancement of Science, 2009, pp. 1451–54, doi:<a href=\"https://doi.org/10.1126/science.1172417\">10.1126/science.1172417</a>.","ama":"Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. <i>Science</i>. 2009;324(5933):1451-1454. doi:<a href=\"https://doi.org/10.1126/science.1172417\">10.1126/science.1172417</a>","ieee":"T.-F. Hsieh <i>et al.</i>, “Genome-wide demethylation of Arabidopsis endosperm,” <i>Science</i>, vol. 324, no. 5933. American Association for the Advancement of Science, pp. 1451–1454, 2009.","apa":"Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R. L., &#38; Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1172417\">https://doi.org/10.1126/science.1172417</a>","short":"T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer, D. Zilberman, Science 324 (2009) 1451–1454.","ista":"Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933), 1451–1454."},"date_updated":"2021-12-14T08:53:26Z","page":"1451-1454","month":"06","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","year":"2009","publication":"Science","quality_controlled":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_processing_charge":"No","author":[{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"first_name":"Christian A.","last_name":"Ibarra","full_name":"Ibarra, Christian A."},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"last_name":"Eshed-Williams","first_name":"Leor","full_name":"Eshed-Williams, Leor"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"title":"Genome-wide demethylation of Arabidopsis endosperm","type":"journal_article","date_published":"2009-06-12T00:00:00Z","status":"public","publication_status":"published","day":"12","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1126/science.1172417","issue":"5933","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/"}],"extern":"1","oa":1,"keyword":["Multidisciplinary"],"external_id":{"pmid":["19520962"]},"scopus_import":"1","intvolume":"       324","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.","lang":"eng"}],"article_type":"original","volume":324,"date_created":"2021-06-04T08:55:41Z"},{"date_created":"2021-06-04T11:49:32Z","volume":456,"article_type":"letter_note","abstract":[{"text":"Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","intvolume":"       456","scopus_import":"1","external_id":{"pmid":["18815594"]},"keyword":["Multidisciplinary"],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/","open_access":"1"}],"oa":1,"extern":"1","issue":"7218","doi":"10.1038/nature07324","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"day":"06","publication_status":"published","status":"public","date_published":"2008-11-06T00:00:00Z","type":"journal_article","title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"},{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"last_name":"Ballinger","first_name":"Tracy","full_name":"Ballinger, Tracy"},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"quality_controlled":"1","publication":"Nature","year":"2008","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"11","page":"125-129","_id":"9457","citation":{"ista":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.","apa":"Zilberman, D., Coleman-Derr, D., Ballinger, T., &#38; Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>","ieee":"D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” <i>Nature</i>, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.","ama":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. 2008;456(7218):125-129. doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>","mla":"Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>.","chicago":"Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>. Springer Nature, 2008. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>."},"date_updated":"2021-12-14T08:54:36Z"},{"author":[{"orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel"}],"title":"The evolving functions of DNA methylation","date_published":"2008-10-01T00:00:00Z","type":"journal_article","publication":"Current Opinion in Plant Biology","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["1369-5266"]},"year":"2008","language":[{"iso":"eng"}],"publisher":"Elsevier ","page":"554-559","_id":"9537","citation":{"chicago":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current Opinion in Plant Biology</i>. Elsevier , 2008. <a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">https://doi.org/10.1016/j.pbi.2008.07.004</a>.","ista":"Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559.","apa":"Zilberman, D. (2008). The evolving functions of DNA methylation. <i>Current Opinion in Plant Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">https://doi.org/10.1016/j.pbi.2008.07.004</a>","short":"D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.","ieee":"D. Zilberman, “The evolving functions of DNA methylation,” <i>Current Opinion in Plant Biology</i>, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.","mla":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current Opinion in Plant Biology</i>, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:<a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">10.1016/j.pbi.2008.07.004</a>.","ama":"Zilberman D. The evolving functions of DNA methylation. <i>Current Opinion in Plant Biology</i>. 2008;11(5):554-559. doi:<a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">10.1016/j.pbi.2008.07.004</a>"},"date_updated":"2021-12-14T08:54:07Z","month":"10","oa_version":"None","pmid":1,"article_type":"review","date_created":"2021-06-08T13:13:37Z","volume":11,"abstract":[{"lang":"eng","text":"DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more."}],"scopus_import":"1","external_id":{"pmid":["18774331"]},"intvolume":"        11","issue":"5","extern":"1","publication_status":"published","status":"public","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1016/j.pbi.2008.07.004"},{"publication_status":"published","status":"public","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1073/pnas.0701861104","day":"17","issue":"16","main_file_link":[{"url":"https://doi.org/10.1073/pnas.0701861104","open_access":"1"}],"oa":1,"extern":"1","scopus_import":"1","external_id":{"pmid":["17409185"]},"intvolume":"       104","oa_version":"Published Version","pmid":1,"article_type":"original","date_created":"2021-06-07T09:38:21Z","volume":104,"abstract":[{"lang":"eng","text":"Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation."}],"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","citation":{"chicago":"Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>.","ista":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757.","apa":"Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &#38; Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>","short":"J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.","ieee":"J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.","mla":"Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16, National Academy of Sciences, 2007, pp. 6752–57, doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>.","ama":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(16):6752-6757. doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>"},"_id":"9487","page":"6752-6757","date_updated":"2021-12-14T08:55:12Z","month":"04","year":"2007","publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"full_name":"Penterman, Jon","last_name":"Penterman","first_name":"Jon"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649"},{"first_name":"Jin Hoe","last_name":"Huh","full_name":"Huh, Jin Hoe"},{"last_name":"Ballinger","first_name":"Tracy","full_name":"Ballinger, Tracy"},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"title":"DNA demethylation in the Arabidopsis genome","date_published":"2007-04-17T00:00:00Z","type":"journal_article"},{"oa_version":"None","author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"title":"The human promoter methylome","pmid":1,"date_created":"2021-06-07T12:08:24Z","date_published":"2007-04-01T00:00:00Z","volume":39,"type":"other_academic_publication","publication":"Nature Genetics","external_id":{"pmid":["17392803"]},"article_processing_charge":"No","quality_controlled":"1","intvolume":"        39","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"issue":"4","year":"2007","extern":"1","publication_status":"published","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","_id":"9504","page":"442-443","date_updated":"2021-12-14T08:55:46Z","citation":{"ama":"Zilberman D. <i>The Human Promoter Methylome</i>. Vol 39. Nature Publishing Group; 2007:442-443. doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>","mla":"Zilberman, Daniel. “The Human Promoter Methylome.” <i>Nature Genetics</i>, vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>.","ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.","apa":"Zilberman, D. (2007). <i>The human promoter methylome</i>. <i>Nature Genetics</i> (Vol. 39, pp. 442–443). Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>","short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.","chicago":"Zilberman, Daniel. <i>The Human Promoter Methylome</i>. <i>Nature Genetics</i>. Vol. 39. Nature Publishing Group, 2007. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>."},"status":"public","month":"04","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1038/ng0407-442","day":"01"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.001131"}],"extern":"1","issue":"22","day":"15","doi":"10.1242/dev.001131","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"status":"public","publication_status":"published","abstract":[{"text":"Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.","lang":"eng"}],"date_created":"2021-06-08T06:29:50Z","volume":134,"article_type":"review","pmid":1,"oa_version":"Published Version","intvolume":"       134","external_id":{"pmid":["17928417"]},"scopus_import":"1","year":"2007","month":"11","_id":"9524","citation":{"mla":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>, vol. 134, no. 22, The Company of Biologists, 2007, pp. 3959–65, doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>.","ama":"Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. <i>Development</i>. 2007;134(22):3959-3965. doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>","ieee":"D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,” <i>Development</i>, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965, 2007.","short":"D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.","apa":"Zilberman, D., &#38; Henikoff, S. (2007). Genome-wide analysis of DNA methylation patterns. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>","ista":"Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development. 134(22), 3959–3965.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>. The Company of Biologists, 2007. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>."},"page":"3959-3965","date_updated":"2021-12-14T08:57:58Z","publisher":"The Company of Biologists","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2007-11-15T00:00:00Z","title":"Genome-wide analysis of DNA methylation patterns","author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"quality_controlled":"1","article_processing_charge":"No","publication":"Development"},{"issue":"1","extern":"1","publication_status":"published","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"doi":"10.1038/ng1929","day":"26","oa_version":"None","pmid":1,"article_type":"original","date_created":"2021-06-07T12:19:31Z","volume":39,"abstract":[{"text":"Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.","lang":"eng"}],"scopus_import":"1","external_id":{"pmid":["17128275"]},"intvolume":"        39","year":"2006","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","date_updated":"2021-12-14T09:02:51Z","_id":"9505","citation":{"ieee":"D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.","mla":"Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69, doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>.","ama":"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. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>","ista":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69.","short":"D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.","apa":"Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>","chicago":"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.” <i>Nature Genetics</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>."},"page":"61-69","month":"11","author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"full_name":"Gehring, Mary","first_name":"Mary","last_name":"Gehring"},{"full_name":"Tran, Robert K.","first_name":"Robert K.","last_name":"Tran"},{"full_name":"Ballinger, Tracy","first_name":"Tracy","last_name":"Ballinger"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"}],"title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","date_published":"2006-11-26T00:00:00Z","type":"journal_article","publication":"Nature Genetics","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]}}]