[{"publication_status":"published","intvolume":"        89","date_created":"2018-12-11T11:46:55Z","publisher":"Cambridge University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"517","page":"475 - 477","doi":"10.1017/S0016672308009683","date_updated":"2024-02-14T09:51:09Z","citation":{"ieee":"N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” <i>Genetics Research</i>, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.","chicago":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” <i>Genetics Research</i>. Cambridge University Press, 2008. <a href=\"https://doi.org/10.1017/S0016672308009683\">https://doi.org/10.1017/S0016672308009683</a>.","ama":"Barton NH. Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics Research</i>. 2008;89(5-6):475-477. doi:<a href=\"https://doi.org/10.1017/S0016672308009683\">10.1017/S0016672308009683</a>","mla":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” <i>Genetics Research</i>, vol. 89, no. 5–6, Cambridge University Press, 2008, pp. 475–77, doi:<a href=\"https://doi.org/10.1017/S0016672308009683\">10.1017/S0016672308009683</a>.","short":"N.H. Barton, Genetics Research 89 (2008) 475–477.","apa":"Barton, N. H. (2008). Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672308009683\">https://doi.org/10.1017/S0016672308009683</a>","ista":"Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477."},"publication":"Genetics Research","oa_version":"None","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"month":"10","scopus_import":"1","article_processing_charge":"No","issue":"5-6","year":"2008","day":"29","quality_controlled":"1","title":"Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin","status":"public","date_published":"2008-10-29T00:00:00Z","publist_id":"7302","volume":89},{"year":"2008","issue":"7218","volume":456,"external_id":{"pmid":["18815594"]},"title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","day":"06","date_created":"2021-06-04T11:49:32Z","pmid":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/"}],"department":[{"_id":"DaZi"}],"citation":{"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.","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.","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>","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.","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","_id":"9457","scopus_import":"1","article_processing_charge":"No","month":"11","author":[{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Devin","full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr"},{"first_name":"Tracy","last_name":"Ballinger","full_name":"Ballinger, Tracy"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"abstract":[{"lang":"eng","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."}],"date_published":"2008-11-06T00:00:00Z","status":"public","article_type":"letter_note","quality_controlled":"1","oa":1,"publisher":"Springer Nature","intvolume":"       456","extern":"1","language":[{"iso":"eng"}],"publication":"Nature","oa_version":"Submitted Version","doi":"10.1038/nature07324","page":"125-129","type":"journal_article","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"keyword":["Multidisciplinary"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"publisher":"Elsevier ","intvolume":"        11","extern":"1","publication":"Current Opinion in Plant Biology","oa_version":"None","language":[{"iso":"eng"}],"page":"554-559","doi":"10.1016/j.pbi.2008.07.004","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["1369-5266"]},"type":"journal_article","article_processing_charge":"No","scopus_import":"1","author":[{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"month":"10","date_published":"2008-10-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"article_type":"review","status":"public","quality_controlled":"1","date_created":"2021-06-08T13:13:37Z","pmid":1,"publication_status":"published","citation":{"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>","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>.","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>.","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>","ista":"Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559.","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."},"department":[{"_id":"DaZi"}],"_id":"9537","date_updated":"2021-12-14T08:54:07Z","issue":"5","year":"2008","volume":11,"external_id":{"pmid":["18774331"]},"title":"The evolving functions of DNA methylation"},{"author":[{"last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"},{"full_name":"Dickinson, Hugh G.","last_name":"Dickinson","first_name":"Hugh G."}],"month":"10","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","article_type":"original","status":"public","date_published":"2007-10-01T00:00:00Z","abstract":[{"text":"The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways.","lang":"eng"}],"intvolume":"        23","publisher":"Elsevier BV","publication_identifier":{"issn":["0168-9525"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Genetics"],"type":"journal_article","doi":"10.1016/j.tig.2007.08.005","page":"503-510","oa_version":"None","publication":"Trends in Genetics","language":[{"iso":"eng"}],"extern":"1","issue":"10","year":"2007","title":"Packaging the male germline in plants","external_id":{"pmid":["17825943"]},"volume":23,"acknowledgement":"X.F. holds a Clarendon Scholarship from the University of Oxford. We thank Angela Hay and Jill Harrison for helpful advice and discussion.","publication_status":"published","pmid":1,"date_created":"2023-01-16T09:22:44Z","_id":"12201","date_updated":"2023-05-08T10:58:47Z","citation":{"short":"X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.","apa":"Feng, X., &#38; Dickinson, H. G. (2007). Packaging the male germline in plants. <i>Trends in Genetics</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>","ista":"Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>. Elsevier BV, 2007. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>.","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>.","ama":"Feng X, Dickinson HG. Packaging the male germline in plants. <i>Trends in Genetics</i>. 2007;23(10):503-510. doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>","ieee":"X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” <i>Trends in Genetics</i>, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007."},"department":[{"_id":"XiFe"}]},{"volume":104,"external_id":{"pmid":["17409185"]},"title":"DNA demethylation in the Arabidopsis genome","day":"17","year":"2007","issue":"16","department":[{"_id":"DaZi"}],"citation":{"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.","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>","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.","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>.","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>","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."},"date_updated":"2021-12-14T08:55:12Z","_id":"9487","date_created":"2021-06-07T09:38:21Z","pmid":1,"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1073/pnas.0701861104","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"date_published":"2007-04-17T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","month":"04","author":[{"last_name":"Penterman","full_name":"Penterman, Jon","first_name":"Jon"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":"Jin Hoe","last_name":"Huh","full_name":"Huh, Jin Hoe"},{"first_name":"Tracy","last_name":"Ballinger","full_name":"Ballinger, Tracy"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"extern":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.0701861104","page":"6752-6757","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publisher":"National Academy of Sciences","oa":1,"intvolume":"       104"},{"article_processing_charge":"No","author":[{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"month":"04","issue":"4","year":"2007","external_id":{"pmid":["17392803"]},"status":"public","quality_controlled":"1","day":"01","title":"The human promoter methylome","volume":39,"date_published":"2007-04-01T00:00:00Z","publication_status":"published","date_created":"2021-06-07T12:08:24Z","publisher":"Nature Publishing Group","pmid":1,"intvolume":"        39","_id":"9504","page":"442-443","doi":"10.1038/ng0407-442","date_updated":"2021-12-14T08:55:46Z","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"other_academic_publication","extern":"1","citation":{"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>.","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>.","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>","short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.","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>","ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443."},"publication":"Nature Genetics","oa_version":"None","department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}]},{"_id":"9524","date_updated":"2021-12-14T08:57:58Z","citation":{"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>.","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."},"department":[{"_id":"DaZi"}],"main_file_link":[{"url":"https://doi.org/10.1242/dev.001131","open_access":"1"}],"publication_status":"published","pmid":1,"date_created":"2021-06-08T06:29:50Z","day":"15","title":"Genome-wide analysis of DNA methylation patterns","external_id":{"pmid":["17928417"]},"volume":134,"issue":"22","year":"2007","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","doi":"10.1242/dev.001131","page":"3959-3965","publication":"Development","oa_version":"Published Version","language":[{"iso":"eng"}],"extern":"1","intvolume":"       134","oa":1,"publisher":"The Company of Biologists","quality_controlled":"1","article_type":"review","status":"public","date_published":"2007-11-15T00:00:00Z","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"}],"author":[{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"month":"11","scopus_import":"1","article_processing_charge":"No"},{"author":[{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Gehring, Mary","last_name":"Gehring","first_name":"Mary"},{"first_name":"Robert K.","last_name":"Tran","full_name":"Tran, Robert K."},{"first_name":"Tracy","full_name":"Ballinger, Tracy","last_name":"Ballinger"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"month":"11","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","article_type":"original","status":"public","date_published":"2006-11-26T00:00:00Z","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"}],"intvolume":"        39","publisher":"Nature Publishing Group","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","doi":"10.1038/ng1929","page":"61-69","oa_version":"None","publication":"Nature Genetics","language":[{"iso":"eng"}],"extern":"1","issue":"1","year":"2006","day":"26","title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","external_id":{"pmid":["17128275"]},"volume":39,"publication_status":"published","pmid":1,"date_created":"2021-06-07T12:19:31Z","_id":"9505","date_updated":"2021-12-14T09:02:51Z","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.","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>","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.","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>.","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>"},"department":[{"_id":"DaZi"}]},{"year":"2005","issue":"2","volume":15,"title":"DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes","day":"26","external_id":{"pmid":["15668172 "]},"pmid":1,"date_created":"2021-06-07T10:24:30Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2005.01.008","open_access":"1"}],"publication_status":"published","department":[{"_id":"DaZi"}],"citation":{"ieee":"R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” <i>Current Biology</i>, vol. 15, no. 2. Elsevier, pp. 154–159, 2005.","ama":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current Biology</i>. 2005;15(2):154-159. doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">10.1016/j.cub.2005.01.008</a>","mla":"Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” <i>Current Biology</i>, vol. 15, no. 2, Elsevier, 2005, pp. 154–59, doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">10.1016/j.cub.2005.01.008</a>.","chicago":"Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” <i>Current Biology</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">https://doi.org/10.1016/j.cub.2005.01.008</a>.","apa":"Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., &#38; Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">https://doi.org/10.1016/j.cub.2005.01.008</a>","ista":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159.","short":"R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159."},"date_updated":"2021-12-14T09:12:26Z","_id":"9491","month":"01","author":[{"full_name":"Tran, Robert K.","last_name":"Tran","first_name":"Robert K."},{"full_name":"Henikoff, Jorja G.","last_name":"Henikoff","first_name":"Jorja G."},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"last_name":"Ditt","full_name":"Ditt, Renata F.","first_name":"Renata F."},{"last_name":"Jacobsen","full_name":"Jacobsen, Steven E.","first_name":"Steven E."},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"article_processing_charge":"No","scopus_import":"1","abstract":[{"lang":"eng","text":"Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units."}],"date_published":"2005-01-26T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original","intvolume":"        15","oa":1,"publisher":"Elsevier","language":[{"iso":"eng"}],"publication":"Current Biology","oa_version":"Published Version","extern":"1","type":"journal_article","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1016/j.cub.2005.01.008","page":"154-159"},{"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1186/gb-2005-6-11-r90","open_access":"1"}],"date_created":"2021-06-07T13:12:41Z","pmid":1,"date_updated":"2021-12-14T09:09:41Z","_id":"9514","department":[{"_id":"DaZi"}],"citation":{"ieee":"R. K. Tran <i>et al.</i>, “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” <i>Genome Biology</i>, vol. 6, no. 11. Springer Nature, 2005.","ista":"Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), R90.","apa":"Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">https://doi.org/10.1186/gb-2005-6-11-r90</a>","short":"R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005).","ama":"Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>. 2005;6(11). doi:<a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">10.1186/gb-2005-6-11-r90</a>","mla":"Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>, vol. 6, no. 11, R90, Springer Nature, 2005, doi:<a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">10.1186/gb-2005-6-11-r90</a>.","chicago":"Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>. Springer Nature, 2005. <a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">https://doi.org/10.1186/gb-2005-6-11-r90</a>."},"year":"2005","issue":"11","external_id":{"pmid":["16277745"]},"title":"Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis","day":"19","volume":6,"oa":1,"publisher":"Springer Nature","intvolume":"         6","doi":"10.1186/gb-2005-6-11-r90","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"extern":"1","language":[{"iso":"eng"}],"publication":"Genome Biology","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","month":"10","author":[{"full_name":"Tran, Robert K.","last_name":"Tran","first_name":"Robert K."},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"first_name":"Cecilia","full_name":"de Bustos, Cecilia","last_name":"de Bustos"},{"first_name":"Renata F.","full_name":"Ditt, Renata F.","last_name":"Ditt"},{"first_name":"Jorja G.","full_name":"Henikoff, Jorja G.","last_name":"Henikoff"},{"last_name":"Lindroth","full_name":"Lindroth, Anders M.","first_name":"Anders M."},{"full_name":"Delrow, Jeffrey","last_name":"Delrow","first_name":"Jeffrey"},{"first_name":"Tom","full_name":"Boyle, Tom","last_name":"Boyle"},{"full_name":"Kwong, Samson","last_name":"Kwong","first_name":"Samson"},{"first_name":"Terri D.","last_name":"Bryson","full_name":"Bryson, Terri D."},{"last_name":"Jacobsen","full_name":"Jacobsen, Steven E.","first_name":"Steven E."},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"article_number":"R90","status":"public","article_type":"original","quality_controlled":"1","abstract":[{"text":"Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.","lang":"eng"}],"date_published":"2005-10-19T00:00:00Z"},{"issue":"5","year":"2005","volume":15,"external_id":{"pmid":["16085410"]},"title":"Epigenetic inheritance in Arabidopsis: Selective silence","date_created":"2021-06-08T09:05:56Z","pmid":1,"publication_status":"published","citation":{"ieee":"D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.","apa":"Zilberman, D., &#38; Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: Selective silence. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">https://doi.org/10.1016/j.gde.2005.07.002</a>","ista":"Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.","short":"D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562.","mla":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5, Elsevier, 2005, pp. 557–62, doi:<a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">10.1016/j.gde.2005.07.002</a>.","ama":"Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence. <i>Current Opinion in Genetics and Development</i>. 2005;15(5):557-562. doi:<a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">10.1016/j.gde.2005.07.002</a>","chicago":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">https://doi.org/10.1016/j.gde.2005.07.002</a>."},"department":[{"_id":"DaZi"}],"_id":"9529","date_updated":"2021-12-14T09:13:13Z","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"month":"10","date_published":"2005-10-01T00:00:00Z","abstract":[{"text":"Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes.","lang":"eng"}],"article_type":"review","status":"public","quality_controlled":"1","publisher":"Elsevier","intvolume":"        15","extern":"1","publication":"Current Opinion in Genetics and Development","oa_version":"None","language":[{"iso":"eng"}],"page":"557-562","doi":"10.1016/j.gde.2005.07.002","publication_identifier":{"issn":["0959-437X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article"},{"author":[{"first_name":"Zhihua","full_name":"Liao, Zhihua","last_name":"Liao"},{"full_name":"Chen, Min","last_name":"Chen","first_name":"Min"},{"first_name":"Yifu","full_name":"Gong, Yifu","last_name":"Gong"},{"full_name":"Guo, Liang","last_name":"Guo","first_name":"Liang"},{"full_name":"Tan, Qiumin","last_name":"Tan","first_name":"Qiumin"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"},{"first_name":"Xiaofen","last_name":"Sun","full_name":"Sun, Xiaofen"},{"first_name":"Feng","last_name":"Tan","full_name":"Tan, Feng"},{"full_name":"Tang, Kexuan","last_name":"Tang","first_name":"Kexuan"}],"scopus_import":"1","article_processing_charge":"No","quality_controlled":"1","article_type":"original","status":"public","date_published":"2004-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs."}],"intvolume":"        15","publisher":"Informa UK Limited","keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"publication_identifier":{"issn":["1042-5179"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1080/10425170410001667348","page":"153-158","publication":"DNA Sequence","oa_version":"None","language":[{"iso":"eng"}],"extern":"1","issue":"2","year":"2004","title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","external_id":{"pmid":["15352294"]},"volume":15,"acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","publication_status":"published","pmid":1,"date_created":"2023-01-16T09:24:50Z","_id":"12203","date_updated":"2023-05-08T10:58:29Z","citation":{"ieee":"Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.","mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>","chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>.","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.","apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>","short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158."},"department":[{"_id":"XiFe"}]},{"doi":"10.1126/science.1095989","page":"1336","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"keyword":["Multidisciplinary"],"type":"journal_article","extern":"1","publication":"Science","oa_version":"None","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","intvolume":"       303","article_type":"original","status":"public","quality_controlled":"1","date_published":"2004-02-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Chan","full_name":"Chan, Simon W.-L.","first_name":"Simon W.-L."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":" Zhixin","full_name":"Xie,  Zhixin","last_name":"Xie"},{"first_name":" Lisa K.","full_name":"Johansen,  Lisa K.","last_name":"Johansen"},{"first_name":"James C.","full_name":"Carrington, James C.","last_name":"Carrington"},{"first_name":"Steven E.","full_name":"Jacobsen, Steven E.","last_name":"Jacobsen"}],"month":"02","_id":"9454","date_updated":"2021-12-14T09:13:53Z","citation":{"ieee":"S. W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” <i>Science</i>, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004.","chicago":"Chan, Simon W.-L., Daniel Zilberman,  Zhixin Xie,  Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2004. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>.","mla":"Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>, vol. 303, no. 5662, American Association for the Advancement of Science, 2004, p. 1336, doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>.","ama":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. <i>Science</i>. 2004;303(5662):1336. doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>","short":"S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.","ista":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336.","apa":"Chan, S. W.-L., Zilberman, D., Xie,  Zhixin, Johansen,  Lisa K., Carrington, J. C., &#38; Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>"},"department":[{"_id":"DaZi"}],"publication_status":"published","date_created":"2021-06-04T11:12:35Z","pmid":1,"external_id":{"pmid":["14988555"]},"day":"27","title":"RNA silencing genes control de novo DNA methylation","volume":303,"issue":"5662","year":"2004"},{"intvolume":"        14","publisher":"Elsevier","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Current Biology","extern":"1","type":"journal_article","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1016/j.cub.2004.06.055","page":"1214-1220","month":"07","author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"full_name":"Cao, Xiaofeng","last_name":"Cao","first_name":"Xiaofeng"},{"first_name":"Lisa K.","full_name":"Johansen, Lisa K.","last_name":"Johansen"},{"first_name":"Zhixin","full_name":"Xie, Zhixin","last_name":"Xie"},{"last_name":"Carrington","full_name":"Carrington, James C.","first_name":"James C."},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."}],"scopus_import":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene \"trigger\" and any other homologous DNA sequences--\"targets\". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production."}],"date_published":"2004-07-13T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original","pmid":1,"date_created":"2021-06-07T10:33:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2004.06.055"}],"publication_status":"published","department":[{"_id":"DaZi"}],"citation":{"ieee":"D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” <i>Current Biology</i>, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004.","short":"D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.","apa":"Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &#38; Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>","ista":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220.","chicago":"Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>.","mla":"Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>.","ama":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. 2004;14(13):1214-1220. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>"},"date_updated":"2021-12-14T08:52:00Z","_id":"9493","year":"2004","issue":"13","volume":14,"title":"Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats","day":"13","external_id":{"pmid":["15242620 "]}},{"_id":"9511","date_updated":"2021-12-14T08:44:24Z","citation":{"ista":"Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.","apa":"Zilberman, D., &#38; Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>","short":"D. Zilberman, S. Henikoff, Genome Biology 5 (2004).","mla":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>, vol. 5, no. 12, 249, Springer Nature, 2004, doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>.","ama":"Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. 2004;5(12). doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>","chicago":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>.","ieee":"D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” <i>Genome Biology</i>, vol. 5, no. 12. Springer Nature, 2004."},"department":[{"_id":"DaZi"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/gb-2004-5-12-249"}],"date_created":"2021-06-07T12:58:06Z","pmid":1,"external_id":{"pmid":["15575975"]},"day":"16","title":"Silencing of transposons in plant genomes: kick them when they're down","volume":5,"issue":"12","year":"2004","doi":"10.1186/gb-2004-5-12-249","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"type":"journal_article","extern":"1","publication":"Genome Biology","oa_version":"Published Version","language":[{"iso":"eng"}],"oa":1,"publisher":"Springer Nature","intvolume":"         5","article_type":"review","status":"public","quality_controlled":"1","date_published":"2004-11-16T00:00:00Z","abstract":[{"lang":"eng","text":"Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it."}],"article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"}],"month":"11","article_number":"249"},{"issue":"5","year":"2004","external_id":{"pmid":["15024409"]},"day":"24","title":"Genetic and functional diversification of small RNA pathways in plants","volume":2,"main_file_link":[{"url":"https://doi.org/10.1371/journal.pbio.0020104","open_access":"1"}],"publication_status":"published","date_created":"2021-06-07T14:12:08Z","pmid":1,"_id":"9517","date_updated":"2021-12-14T08:43:57Z","citation":{"apa":"Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification of small RNA pathways in plants. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.0020104\">https://doi.org/10.1371/journal.pbio.0020104</a>","ista":"Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biology. 2(5), 0642–0652.","short":"Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman, S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.","ama":"Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. <i>PLoS Biology</i>. 2004;2(5):0642-0652. doi:<a href=\"https://doi.org/10.1371/journal.pbio.0020104\">10.1371/journal.pbio.0020104</a>","mla":"Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” <i>PLoS Biology</i>, vol. 2, no. 5, Public Library of Science, 2004, pp. 0642–52, doi:<a href=\"https://doi.org/10.1371/journal.pbio.0020104\">10.1371/journal.pbio.0020104</a>.","chicago":"Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D.  Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. “Genetic and Functional Diversification of Small RNA Pathways in Plants.” <i>PLoS Biology</i>. Public Library of Science, 2004. <a href=\"https://doi.org/10.1371/journal.pbio.0020104\">https://doi.org/10.1371/journal.pbio.0020104</a>.","ieee":"Z. Xie <i>et al.</i>, “Genetic and functional diversification of small RNA pathways in plants,” <i>PLoS Biology</i>, vol. 2, no. 5. Public Library of Science, pp. 0642–0652, 2004."},"department":[{"_id":"DaZi"}],"article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Xie","full_name":"Xie, Zhixin","first_name":"Zhixin"},{"first_name":"Lisa K.","last_name":"Johansen","full_name":"Johansen, Lisa K."},{"last_name":"Gustafson","full_name":"Gustafson, Adam M.","first_name":"Adam M."},{"first_name":"Kristin D.","full_name":"Kasschau, Kristin D.","last_name":"Kasschau"},{"first_name":"Andrew D. ","full_name":"Lellis, Andrew D. ","last_name":"Lellis"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."},{"first_name":"James C.","last_name":"Carrington","full_name":"Carrington, James C."}],"month":"02","article_type":"original","status":"public","quality_controlled":"1","date_published":"2004-02-24T00:00:00Z","abstract":[{"lang":"eng","text":"Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense."}],"oa":1,"publisher":"Public Library of Science","intvolume":"         2","doi":"10.1371/journal.pbio.0020104","page":"0642-0652","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","extern":"1","oa_version":"Published Version","publication":"PLoS Biology","language":[{"iso":"eng"}]},{"publication":"Science","oa_version":"None","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"keyword":["Multidisciplinary"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","page":"716-719","doi":"10.1126/science.1079695","intvolume":"       299","publisher":"American Association for the Advancement of Science","date_published":"2003-01-31T00:00:00Z","abstract":[{"text":"Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation.","lang":"eng"}],"quality_controlled":"1","article_type":"original","status":"public","author":[{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"last_name":"Cao","full_name":"Cao,  Xiaofeng","first_name":" Xiaofeng"},{"last_name":"Jacobsen","full_name":"Jacobsen, Steven E.","first_name":"Steven E."}],"month":"01","scopus_import":"1","article_processing_charge":"No","citation":{"ieee":"D. Zilberman,  Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation,” <i>Science</i>, vol. 299, no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003.","short":"D. Zilberman,  Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719.","ista":"Zilberman D, Cao  Xiaofeng, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 299(5607), 716–719.","apa":"Zilberman, D., Cao,  Xiaofeng, &#38; Jacobsen, S. E. (2003). ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1079695\">https://doi.org/10.1126/science.1079695</a>","chicago":"Zilberman, Daniel,  Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2003. <a href=\"https://doi.org/10.1126/science.1079695\">https://doi.org/10.1126/science.1079695</a>.","mla":"Zilberman, Daniel, et al. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” <i>Science</i>, vol. 299, no. 5607, American Association for the Advancement of Science, 2003, pp. 716–19, doi:<a href=\"https://doi.org/10.1126/science.1079695\">10.1126/science.1079695</a>.","ama":"Zilberman D, Cao  Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. <i>Science</i>. 2003;299(5607):716-719. doi:<a href=\"https://doi.org/10.1126/science.1079695\">10.1126/science.1079695</a>"},"department":[{"_id":"DaZi"}],"_id":"9455","date_updated":"2021-12-14T08:43:30Z","pmid":1,"date_created":"2021-06-04T11:26:26Z","publication_status":"published","volume":299,"day":"31","title":"ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation","external_id":{"pmid":["12522258"]},"issue":"5607","year":"2003"},{"external_id":{"pmid":["14680640"]},"day":"16","title":"Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation","volume":13,"issue":"24","year":"2003","_id":"9495","date_updated":"2021-12-14T08:41:38Z","citation":{"ieee":"X. Cao <i>et al.</i>, “Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation,” <i>Current Biology</i>, vol. 13, no. 24. Elsevier, pp. 2212–2217, 2003.","chicago":"Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” <i>Current Biology</i>. Elsevier, 2003. <a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">https://doi.org/10.1016/j.cub.2003.11.052</a>.","mla":"Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” <i>Current Biology</i>, vol. 13, no. 24, Elsevier, 2003, pp. 2212–17, doi:<a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">10.1016/j.cub.2003.11.052</a>.","ama":"Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. <i>Current Biology</i>. 2003;13(24):2212-2217. doi:<a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">10.1016/j.cub.2003.11.052</a>","short":"X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E. Jacobsen, Current Biology 13 (2003) 2212–2217.","ista":"Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. 2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. 13(24), 2212–2217.","apa":"Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M., &#38; Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2003.11.052\">https://doi.org/10.1016/j.cub.2003.11.052</a>"},"department":[{"_id":"DaZi"}],"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2003.11.052","open_access":"1"}],"date_created":"2021-06-07T10:43:02Z","pmid":1,"article_type":"original","status":"public","quality_controlled":"1","date_published":"2003-12-16T00:00:00Z","abstract":[{"lang":"eng","text":"RNA interference is a conserved process in which double-stranded RNA is processed into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing. In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to silenced RNA is de novo methylated at its cytosine residues. This methylation is not only at canonical CpG sites but also at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly complete loss of asymmetric methylation and a partial loss of CpNpG methylation. The remaining asymmetric and CpNpG methylation was dependent on the activity of CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation. These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of siRNAs. Finally, we demonstrate that DRM activity is required for the initial establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric sites."}],"article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Xiaofeng","last_name":"Cao","full_name":"Cao, Xiaofeng"},{"last_name":"Aufsatz","full_name":"Aufsatz, Werner","first_name":"Werner"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"first_name":"M.Florian","full_name":"Mette, M.Florian","last_name":"Mette"},{"full_name":"Huang, Michael S.","last_name":"Huang","first_name":"Michael S."},{"first_name":"Marjori","last_name":"Matzke","full_name":"Matzke, Marjori"},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."}],"month":"12","page":"2212-2217","doi":"10.1016/j.cub.2003.11.052","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"type":"journal_article","extern":"1","oa_version":"Published Version","publication":"Current Biology","language":[{"iso":"eng"}],"oa":1,"publisher":"Elsevier","intvolume":"        13"},{"author":[{"first_name":"A. M.","last_name":"Lindroth","full_name":"Lindroth, A. M."},{"full_name":"Cao, Xiaofeng","last_name":"Cao","first_name":"Xiaofeng"},{"full_name":"Jackson, James P.","last_name":"Jackson","first_name":"James P."},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"},{"last_name":"McCallum","full_name":"McCallum, Claire M.","first_name":"Claire M."},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"},{"full_name":"Jacobsen, Steven E.","last_name":"Jacobsen","first_name":"Steven E."}],"month":"06","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","article_type":"original","status":"public","date_published":"2001-06-15T00:00:00Z","abstract":[{"text":"Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent alleles) are associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.","lang":"eng"}],"intvolume":"       292","publisher":"American Association for the Advancement of Science","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Multidisciplinary"],"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"type":"journal_article","page":"2077-2080","doi":"10.1126/science.1059745","publication":"Science","oa_version":"None","language":[{"iso":"eng"}],"extern":"1","issue":"5524","year":"2001","day":"15","title":"Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation","external_id":{"pmid":["11349138"]},"volume":292,"publication_status":"published","pmid":1,"date_created":"2021-06-02T13:35:16Z","_id":"9444","date_updated":"2021-12-14T08:40:32Z","citation":{"chicago":"Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2001. <a href=\"https://doi.org/10.1126/science.1059745\">https://doi.org/10.1126/science.1059745</a>.","ama":"Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. <i>Science</i>. 2001;292(5524):2077-2080. doi:<a href=\"https://doi.org/10.1126/science.1059745\">10.1126/science.1059745</a>","mla":"Lindroth, A. M., et al. “Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation.” <i>Science</i>, vol. 292, no. 5524, American Association for the Advancement of Science, 2001, pp. 2077–80, doi:<a href=\"https://doi.org/10.1126/science.1059745\">10.1126/science.1059745</a>.","short":"A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff, S.E. Jacobsen, Science 292 (2001) 2077–2080.","ista":"Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 292(5524), 2077–2080.","apa":"Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff, S., &#38; Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1059745\">https://doi.org/10.1126/science.1059745</a>","ieee":"A. M. Lindroth <i>et al.</i>, “Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation,” <i>Science</i>, vol. 292, no. 5524. American Association for the Advancement of Science, pp. 2077–2080, 2001."},"department":[{"_id":"DaZi"}]}]