[{"publication_status":"published","department":[{"_id":"MaRo"},{"_id":"DaZi"}],"corr_author":"1","ec_funded":1,"date_published":"2025-09-12T00:00:00Z","year":"2025","status":"public","month":"09","date_created":"2025-10-16T13:11:21Z","isi":1,"author":[{"full_name":"Shahzad, Zaigham","last_name":"Shahzad","first_name":"Zaigham"},{"first_name":"Elizabeth","last_name":"Hollwey","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth"},{"full_name":"Moore, Jonathan D.","last_name":"Moore","first_name":"Jonathan D."},{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"full_name":"Cassin-Ross, Gaëlle","last_name":"Cassin-Ross","first_name":"Gaëlle"},{"full_name":"Rouached, Hatem","first_name":"Hatem","last_name":"Rouached"},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"intvolume":"        11","publication_identifier":{"issn":["2055-0278"]},"OA_place":"publisher","file":[{"date_updated":"2025-10-23T11:13:58Z","date_created":"2025-10-23T11:13:58Z","access_level":"open_access","file_name":"2025_NaturePlants_Shahzad.pdf","success":1,"checksum":"6a3f6cffdc934b8a2015c3c247f5a92a","file_size":7746662,"content_type":"application/pdf","creator":"dernst","file_id":"20524","relation":"main_file"}],"file_date_updated":"2025-10-23T11:13:58Z","oa_version":"Published Version","doi":"10.1038/s41477-025-02108-4","external_id":{"pmid":["40940427"],"isi":["001570197600001"]},"ddc":["580"],"scopus_import":"1","title":"Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank P. Baduel and V. Colot for sharing SV data, A. Muyle for gbM conservation data and X. Feng, C. Dean, E. Coen and Zilberman lab members for constructive comments on the paper. This work was supported by a European Research Council grant (725746) to D.Z., LUMS Startup grant (STG-188) to Z.S. and US National Science Foundation grant (MCB-2334561) to H.R. This study would not have been possible without Arabidopsis 1001 genome, methylome and transcriptome resources. Open access funding provided by Institute of Science and Technology (IST Austria).","pmid":1,"publication":"Nature Plants","page":"2084-2099","OA_type":"hybrid","article_type":"original","_id":"20479","day":"12","publisher":"Springer Nature","citation":{"short":"Z. Shahzad, E. Hollwey, J.D. Moore, J. Choi, G. Cassin-Ross, H. Rouached, M.R. Robinson, D. Zilberman, Nature Plants 11 (2025) 2084–2099.","ama":"Shahzad Z, Hollwey E, Moore JD, et al. Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations. <i>Nature Plants</i>. 2025;11:2084-2099. doi:<a href=\"https://doi.org/10.1038/s41477-025-02108-4\">10.1038/s41477-025-02108-4</a>","mla":"Shahzad, Zaigham, et al. “Gene Body Methylation Regulates Gene Expression and Mediates Phenotypic Diversity in Natural Arabidopsis Populations.” <i>Nature Plants</i>, vol. 11, Springer Nature, 2025, pp. 2084–99, doi:<a href=\"https://doi.org/10.1038/s41477-025-02108-4\">10.1038/s41477-025-02108-4</a>.","ista":"Shahzad Z, Hollwey E, Moore JD, Choi J, Cassin-Ross G, Rouached H, Robinson MR, Zilberman D. 2025. Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations. Nature Plants. 11, 2084–2099.","apa":"Shahzad, Z., Hollwey, E., Moore, J. D., Choi, J., Cassin-Ross, G., Rouached, H., … Zilberman, D. (2025). Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-025-02108-4\">https://doi.org/10.1038/s41477-025-02108-4</a>","chicago":"Shahzad, Zaigham, Elizabeth Hollwey, Jonathan D. Moore, Jaemyung Choi, Gaëlle Cassin-Ross, Hatem Rouached, Matthew Richard Robinson, and Daniel Zilberman. “Gene Body Methylation Regulates Gene Expression and Mediates Phenotypic Diversity in Natural Arabidopsis Populations.” <i>Nature Plants</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41477-025-02108-4\">https://doi.org/10.1038/s41477-025-02108-4</a>.","ieee":"Z. Shahzad <i>et al.</i>, “Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations,” <i>Nature Plants</i>, vol. 11. Springer Nature, pp. 2084–2099, 2025."},"license":"https://creativecommons.org/licenses/by/4.0/","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"project":[{"call_identifier":"H2020","_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":11,"date_updated":"2025-12-01T14:59:10Z","PlanS_conform":"1","abstract":[{"text":"Genetic variation is generally regarded as a prerequisite for evolution. In principle, epigenetic information inherited independently of DNA sequence can also enable evolution, but whether this occurs in natural populations is unknown. Here we show that single-nucleotide and epigenetic gene body DNA methylation (gbM) polymorphisms explain comparable amounts of expression variance in <jats:italic>Arabidopsis thaliana</jats:italic> populations. We genetically demonstrate that gbM regulates transcription, and we identify and genetically validate many associations between gbM polymorphism and the variation of complex traits: fitness under heat and drought, flowering time and accumulation of diverse minerals. Epigenome-wide association studies pinpoint trait-relevant genes with greater precision than genetic association analyses, probably due to reduced linkage disequilibrium between gbM variants. Finally, we identify numerous associations between gbM epialleles and diverse environmental conditions in native habitats, suggesting that gbM facilitates adaptation. Overall, our results indicate that epigenetic methylation variation fundamentally shapes phenotypic diversity in a natural population.","lang":"eng"}],"language":[{"iso":"eng"}]},{"doi":"10.1093/molbev/msaf085","external_id":{"pmid":["40202086"],"isi":["001483460200001"]},"oa_version":"Published Version","file_date_updated":"2025-05-28T09:34:36Z","ddc":["570"],"OA_place":"publisher","file":[{"date_updated":"2025-05-28T09:34:36Z","date_created":"2025-05-28T09:34:36Z","file_name":"2025_MBE_Bett.pdf","access_level":"open_access","file_size":1282772,"checksum":"6c14b03f94b4aadf8869be2c4366d077","success":1,"content_type":"application/pdf","file_id":"19756","creator":"dernst","relation":"main_file"}],"title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes","pmid":1,"publication":"Molecular Biology and Evolution","acknowledgement":"We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA.","department":[{"_id":"BeVi"},{"_id":"DaZi"}],"publication_status":"published","date_published":"2025-05-01T00:00:00Z","corr_author":"1","status":"public","month":"05","year":"2025","author":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","first_name":"Vincent K","last_name":"Bett"},{"last_name":"Trejo Arellano","first_name":"Minerva S","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","full_name":"Trejo Arellano, Minerva S","orcid":"0000-0002-1982-3475"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"intvolume":"        42","date_created":"2025-05-25T22:16:56Z","isi":1,"citation":{"short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>","mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>","chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025."},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","issue":"5","article_number":"msaf085","type":"journal_article","volume":42,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"PAT 8748323","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"abstract":[{"lang":"eng","text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome."}],"language":[{"iso":"eng"}],"date_updated":"2026-04-07T12:28:15Z","DOAJ_listed":"1","OA_type":"gold","article_type":"original","_id":"19735","related_material":{"link":[{"relation":"software","url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git"}],"record":[{"relation":"dissertation_contains","id":"20444","status":"private"},{"relation":"dissertation_contains","status":"public","id":"20449"}]},"publisher":"Oxford University Press","day":"01"},{"language":[{"iso":"eng"}],"abstract":[{"text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.","lang":"eng"}],"date_updated":"2024-10-09T21:06:16Z","volume":81,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","article_number":"102087","issue":"8","citation":{"ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion in Genetics and Development</i>. 2023;81(8). doi:<a href=\"https://doi.org/10.1016/j.gde.2023.102087\">10.1016/j.gde.2023.102087</a>","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023).","mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion in Genetics and Development</i>, vol. 81, no. 8, 102087, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.gde.2023.102087\">10.1016/j.gde.2023.102087</a>.","ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 81(8), 102087.","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” <i>Current Opinion in Genetics and Development</i>, vol. 81, no. 8. Elsevier, 2023.","chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.gde.2023.102087\">https://doi.org/10.1016/j.gde.2023.102087</a>.","apa":"Hollwey, E., Briffa, A., Howard, M., &#38; Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2023.102087\">https://doi.org/10.1016/j.gde.2023.102087</a>"},"day":"01","publisher":"Elsevier","article_type":"original","_id":"13965","pmid":1,"publication":"Current Opinion in Genetics and Development","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","scopus_import":"1","ddc":["570"],"doi":"10.1016/j.gde.2023.102087","oa_version":"Published Version","external_id":{"isi":["001047020200001"],"pmid":["37441873"]},"file_date_updated":"2023-08-07T08:32:26Z","file":[{"relation":"main_file","file_id":"13980","creator":"dernst","content_type":"application/pdf","checksum":"a294cd9506b80ed6ef218ef44ed32765","success":1,"file_size":2568632,"access_level":"open_access","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","date_created":"2023-08-07T08:32:26Z","date_updated":"2023-08-07T08:32:26Z"}],"intvolume":"        81","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"author":[{"first_name":"Elizabeth","last_name":"Hollwey","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"full_name":"Briffa, Amy","last_name":"Briffa","first_name":"Amy"},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"}],"isi":1,"date_created":"2023-08-06T22:01:10Z","month":"08","status":"public","year":"2023","date_published":"2023-08-01T00:00:00Z","corr_author":"1","department":[{"_id":"DaZi"}]},{"article_processing_charge":"Yes (via OA deal)","publication":"Cell Systems","pmid":1,"acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","ddc":["570"],"external_id":{"isi":["001113459100001"],"pmid":["37944515"]},"doi":"10.1016/j.cels.2023.10.007","file_date_updated":"2023-11-20T11:22:52Z","oa_version":"Published Version","file":[{"date_updated":"2023-11-20T11:22:52Z","date_created":"2023-11-20T11:22:52Z","file_name":"2023_CellSystems_Briffa.pdf","access_level":"open_access","file_size":5587897,"success":1,"checksum":"101fdac59e6f1102d68ef91f2b5bd51a","creator":"dernst","file_id":"14580","content_type":"application/pdf","relation":"main_file"}],"quality_controlled":"1","title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","scopus_import":"1","month":"11","status":"public","year":"2023","intvolume":"        14","publication_identifier":{"issn":["2405-4712"],"eissn":["2405-4720"]},"author":[{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth","first_name":"Elizabeth","last_name":"Hollwey"},{"first_name":"Zaigham","last_name":"Shahzad","full_name":"Shahzad, Zaigham"},{"last_name":"Moore","first_name":"Jonathan D.","full_name":"Moore, Jonathan D."},{"first_name":"David B.","last_name":"Lyons","full_name":"Lyons, David B."},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"date_created":"2023-11-19T23:00:54Z","isi":1,"department":[{"_id":"DaZi"}],"publication_status":"published","date_published":"2023-11-15T00:00:00Z","ec_funded":1,"corr_author":"1","volume":14,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"H2020","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.","lang":"eng"}],"date_updated":"2025-09-09T13:28:50Z","citation":{"mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>.","short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. 2023;14(11):953-967. doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., &#38; Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>","ieee":"A. Briffa <i>et al.</i>, “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” <i>Cell Systems</i>, vol. 14, no. 11. Elsevier, pp. 953–967, 2023.","chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>.","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967."},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","issue":"11","_id":"14551","article_type":"original","publisher":"Elsevier","day":"15","page":"953-967"},{"publication":"Cell Reports","acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","article_processing_charge":"Yes","title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","quality_controlled":"1","scopus_import":"1","external_id":{"isi":["000944921600001"]},"doi":"10.1016/j.celrep.2023.112132","oa_version":"Published Version","file_date_updated":"2023-05-11T10:41:42Z","ddc":["580"],"file":[{"relation":"main_file","file_name":"2023_CellReports_Lyons.pdf","access_level":"open_access","date_updated":"2023-05-11T10:41:42Z","date_created":"2023-05-11T10:41:42Z","file_id":"12941","content_type":"application/pdf","creator":"kschuh","file_size":8401261,"checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","success":1}],"author":[{"first_name":"David B.","last_name":"Lyons","full_name":"Lyons, David B."},{"full_name":"Briffa, Amy","first_name":"Amy","last_name":"Briffa"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"first_name":"Elizabeth","last_name":"Hollwey","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"full_name":"Colicchio, Jack","first_name":"Jack","last_name":"Colicchio"},{"last_name":"Anderson","first_name":"Ian","full_name":"Anderson, Ian"},{"first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Martin","last_name":"Howard","full_name":"Howard, Martin"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"intvolume":"        42","publication_identifier":{"eissn":["2211-1247"]},"date_created":"2023-02-23T09:17:44Z","isi":1,"status":"public","month":"03","year":"2023","ec_funded":1,"date_published":"2023-03-28T00:00:00Z","corr_author":"1","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_status":"published","abstract":[{"text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:57:43Z","volume":42,"type":"journal_article","oa":1,"project":[{"call_identifier":"H2020","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","issue":"3","article_number":"112132","citation":{"ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","ieee":"D. B. Lyons <i>et al.</i>, “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” <i>Cell Reports</i>, vol. 42, no. 3. Elsevier, 2023.","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>.","apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>, vol. 42, no. 3, 112132, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>."},"publisher":"Elsevier","day":"28","article_type":"original","_id":"12672"},{"type":"journal_article","volume":10,"keyword":["genetics and molecular biology"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020"}],"oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin."}],"date_updated":"2025-04-14T07:57:42Z","citation":{"apa":"Choi, J., Lyons, D. B., &#38; Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>.","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>, vol. 10, e72676, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>"},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"e72676","_id":"10533","article_type":"original","day":"01","publisher":"eLife Sciences Publications","article_processing_charge":"No","publication":"eLife","pmid":1,"acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","ddc":["570"],"file_date_updated":"2022-05-16T10:42:22Z","oa_version":"Published Version","external_id":{"pmid":["34850679"],"isi":["000754832000001"]},"doi":"10.7554/elife.72676","file":[{"file_size":2715200,"checksum":"22ed4c55fb550f6da02ae55c359be651","success":1,"file_id":"11384","creator":"dernst","content_type":"application/pdf","date_created":"2022-05-16T10:42:22Z","date_updated":"2022-05-16T10:42:22Z","file_name":"2021_eLife_Choi.pdf","access_level":"open_access","relation":"main_file"}],"quality_controlled":"1","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","scopus_import":"1","month":"12","status":"public","year":"2021","intvolume":"        10","publication_identifier":{"issn":["2050-084X"]},"author":[{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"last_name":"Lyons","first_name":"David B","full_name":"Lyons, David B"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"date_created":"2021-12-10T13:12:08Z","isi":1,"department":[{"_id":"DaZi"}],"publication_status":"published","date_published":"2021-12-01T00:00:00Z","ec_funded":1,"corr_author":"1"},{"publisher":"National Academy of Sciences","day":"16","article_type":"original","_id":"9877","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","has_accepted_license":"1","issue":"29","article_number":"e2104445118","citation":{"ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences of the United States of America. 118(29), e2104445118.","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 29. National Academy of Sciences, 2021.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>"},"abstract":[{"text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-05-14T10:59:43Z","type":"journal_article","volume":118,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-07-16T00:00:00Z","department":[{"_id":"DaZi"}],"publication_status":"published","author":[{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"full_name":"Ruan, Deling","last_name":"Ruan","first_name":"Deling"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Sharma","first_name":"Manoj K.","full_name":"Sharma, Manoj K."},{"last_name":"Sharma","first_name":"Rita","full_name":"Sharma, Rita"},{"last_name":"Ye","first_name":"XinYi","full_name":"Ye, XinYi"},{"full_name":"Nguyen, Nicholas D.","first_name":"Nicholas D.","last_name":"Nguyen"},{"full_name":"Nijjar, Sukhranjan","first_name":"Sukhranjan","last_name":"Nijjar"},{"last_name":"Ronald","first_name":"Pamela C.","full_name":"Ronald, Pamela C."},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":"       118","date_created":"2021-08-10T19:30:41Z","isi":1,"status":"public","month":"07","year":"2021","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","file_date_updated":"2021-08-11T09:31:41Z","external_id":{"isi":["000685037700012"],"pmid":["34272287"]},"doi":"10.1073/pnas.2104445118","ddc":["580","570"],"file":[{"date_created":"2021-08-11T09:31:41Z","date_updated":"2021-08-11T09:31:41Z","access_level":"open_access","file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","checksum":"19e84ad8c03c60222744ee8e16cd6998","success":1,"file_size":1898360,"creator":"asandaue","file_id":"9879","content_type":"application/pdf","relation":"main_file"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","pmid":1,"acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","article_processing_charge":"Yes (in subscription journal)"},{"OA_type":"hybrid","page":"310-323.e7","day":"16","publisher":"Elsevier","extern":"1","_id":"9526","article_type":"original","issue":"2","citation":{"chicago":"Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.” <i>Molecular Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molcel.2019.10.011\">https://doi.org/10.1016/j.molcel.2019.10.011</a>.","ieee":"J. Choi, D. B. Lyons, M. Y. Kim, J. D. Moore, and D. Zilberman, “DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts,” <i>Molecular Cell</i>, vol. 77, no. 2. Elsevier, p. 310–323.e7, 2020.","apa":"Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., &#38; Zilberman, D. (2020). DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2019.10.011\">https://doi.org/10.1016/j.molcel.2019.10.011</a>","ista":"Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. 2020. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Molecular Cell. 77(2), 310–323.e7.","mla":"Choi, Jaemyung, et al. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.” <i>Molecular Cell</i>, vol. 77, no. 2, Elsevier, 2020, p. 310–323.e7, doi:<a href=\"https://doi.org/10.1016/j.molcel.2019.10.011\">10.1016/j.molcel.2019.10.011</a>.","ama":"Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. <i>Molecular Cell</i>. 2020;77(2):310-323.e7. doi:<a href=\"https://doi.org/10.1016/j.molcel.2019.10.011\">10.1016/j.molcel.2019.10.011</a>","short":"J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77 (2020) 310–323.e7."},"date_updated":"2024-10-16T12:14:37Z","abstract":[{"text":"DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here, we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation of genes also activates antisense transcription, which is modestly enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","volume":77,"type":"journal_article","date_published":"2020-01-16T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2019.10.011"}],"publication_status":"published","department":[{"_id":"DaZi"}],"date_created":"2021-06-08T06:37:09Z","author":[{"full_name":"Choi, Jaemyung","first_name":"Jaemyung","last_name":"Choi"},{"first_name":"David B.","last_name":"Lyons","full_name":"Lyons, David B."},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"full_name":"Moore, Jonathan D.","last_name":"Moore","first_name":"Jonathan D."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"}],"intvolume":"        77","publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"year":"2020","status":"public","month":"01","scopus_import":"1","title":"DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts","quality_controlled":"1","OA_place":"publisher","oa_version":"Published Version","external_id":{"pmid":["31732458"]},"doi":"10.1016/j.molcel.2019.10.011","publication":"Molecular Cell","pmid":1,"article_processing_charge":"No"},{"year":"2019","status":"public","month":"05","date_created":"2021-06-04T12:38:20Z","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"full_name":"Ono, Akemi","first_name":"Akemi","last_name":"Ono"},{"last_name":"Scholten","first_name":"Stefan","full_name":"Scholten, Stefan"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Takashi","last_name":"Okamoto","full_name":"Okamoto, Takashi"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"intvolume":"       116","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","department":[{"_id":"DaZi"}],"date_published":"2019-05-07T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Proceedings of the National Academy of Sciences","file":[{"checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","success":1,"file_size":1142540,"creator":"asandaue","file_id":"9461","content_type":"application/pdf","date_updated":"2021-06-04T12:50:47Z","date_created":"2021-06-04T12:50:47Z","access_level":"open_access","file_name":"2019_PNAS_Kim.pdf","relation":"main_file"}],"oa_version":"Published Version","file_date_updated":"2021-06-04T12:50:47Z","doi":"10.1073/pnas.1821435116","external_id":{"pmid":["31000601"]},"ddc":["580"],"scopus_import":"1","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","quality_controlled":"1","article_type":"original","_id":"9460","day":"07","publisher":"National Academy of Sciences","extern":"1","page":"9652-9657","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Multidisciplinary"],"type":"journal_article","volume":116,"date_updated":"2021-12-14T07:52:30Z","abstract":[{"text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>.","ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>"},"issue":"19","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1"},{"status":"public","month":"10","year":"2019","author":[{"full_name":"Harris, Keith D.","last_name":"Harris","first_name":"Keith D."},{"last_name":"Lloyd","first_name":"James P. B.","full_name":"Lloyd, James P. B."},{"full_name":"Domb, Katherine","last_name":"Domb","first_name":"Katherine"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"},{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"}],"publication_identifier":{"eissn":["1756-8935"]},"intvolume":"        12","date_created":"2021-06-08T09:21:51Z","department":[{"_id":"DaZi"}],"publication_status":"published","date_published":"2019-10-10T00:00:00Z","article_processing_charge":"No","publication":"Epigenetics and Chromatin","pmid":1,"oa_version":"Published Version","file_date_updated":"2021-06-08T09:29:19Z","external_id":{"pmid":["31601251"]},"doi":"10.1186/s13072-019-0307-4","ddc":["570"],"file":[{"date_updated":"2021-06-08T09:29:19Z","date_created":"2021-06-08T09:29:19Z","access_level":"open_access","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","success":1,"checksum":"86ff50a7517891511af2733c76c81b67","file_size":3221067,"file_id":"9531","creator":"asandaue","content_type":"application/pdf","relation":"main_file"}],"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","quality_controlled":"1","scopus_import":"1","_id":"9530","article_type":"original","extern":"1","publisher":"Springer Nature","day":"10","type":"journal_article","volume":12,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T07:53:00Z","citation":{"ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &#38; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” <i>Epigenetics and Chromatin</i>, vol. 12. Springer Nature, 2019.","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>.","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>, vol. 12, 62, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>."},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"62"},{"_id":"9471","article_type":"original","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/187674 "}]},"extern":"1","day":"15","publisher":"National Academy of Sciences","page":"E4720-E4729","type":"journal_article","volume":115,"keyword":["Multidisciplinary"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin."}],"date_updated":"2021-12-14T07:53:40Z","citation":{"apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>","ieee":"J. M. Frost <i>et al.</i>, “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>.","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(20):E4720-E4729. doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>"},"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","issue":"20","month":"05","status":"public","year":"2018","intvolume":"       115","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"full_name":"Frost, Jennifer M.","last_name":"Frost","first_name":"Jennifer M."},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"full_name":"Park, Guen Tae","first_name":"Guen Tae","last_name":"Park"},{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"first_name":"Miyuki","last_name":"Nakamura","full_name":"Nakamura, Miyuki"},{"first_name":"Samuel J. H.","last_name":"Lin","full_name":"Lin, Samuel J. H."},{"full_name":"Yoo, Hyunjin","first_name":"Hyunjin","last_name":"Yoo"},{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"full_name":"Ikeda, Yoko","first_name":"Yoko","last_name":"Ikeda"},{"last_name":"Kinoshita","first_name":"Tetsu","full_name":"Kinoshita, Tetsu"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"date_created":"2021-06-07T06:11:28Z","department":[{"_id":"DaZi"}],"publication_status":"published","date_published":"2018-05-15T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Proceedings of the National Academy of Sciences","ddc":["580"],"file_date_updated":"2021-06-07T06:16:38Z","external_id":{"pmid":["29712855"]},"doi":"10.1073/pnas.1713333115","oa_version":"Published Version","file":[{"relation":"main_file","success":1,"checksum":"810260dc0e3cc3033e15c19ad0dc123e","file_size":3045260,"file_id":"9472","content_type":"application/pdf","creator":"asandaue","date_updated":"2021-06-07T06:16:38Z","date_created":"2021-06-07T06:16:38Z","access_level":"open_access","file_name":"2018_PNAS_Frost.pdf"}],"quality_controlled":"1","title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","scopus_import":"1"},{"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"e30674","citation":{"chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","apa":"Lyons, D. B., &#38; Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.30674\">https://doi.org/10.7554/elife.30674</a>","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” <i>ELife</i>, vol. 6, e30674, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.30674\">10.7554/elife.30674</a>","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017)."},"abstract":[{"text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T07:54:36Z","type":"journal_article","volume":6,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","day":"15","publisher":"eLife Sciences Publications","article_type":"original","_id":"9445","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","quality_controlled":"1","scopus_import":"1","file_date_updated":"2021-06-02T14:33:36Z","external_id":{"pmid":["29140247"]},"oa_version":"Published Version","doi":"10.7554/elife.30674","ddc":["570"],"file":[{"file_name":"2017_eLife_Lyons.pdf","access_level":"open_access","date_created":"2021-06-02T14:33:36Z","date_updated":"2021-06-02T14:33:36Z","file_id":"9446","content_type":"application/pdf","creator":"cziletti","file_size":1603102,"success":1,"checksum":"4cfcdd67511ae4aed3d993550e46e146","relation":"main_file"}],"publication":"eLife","pmid":1,"article_processing_charge":"No","date_published":"2017-11-15T00:00:00Z","department":[{"_id":"DaZi"}],"publication_status":"published","author":[{"last_name":"Lyons","first_name":"David B","full_name":"Lyons, David B"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"publication_identifier":{"eissn":["2050-084X"]},"intvolume":"         6","date_created":"2021-06-02T14:28:58Z","status":"public","month":"11","year":"2017"},{"publication":"Genome Biology","pmid":1,"article_processing_charge":"No","title":"An evolutionary case for functional gene body methylation in plants and animals","quality_controlled":"1","scopus_import":"1","file_date_updated":"2021-06-07T12:31:36Z","oa_version":"Published Version","external_id":{"pmid":["28486944"]},"doi":"10.1186/s13059-017-1230-2","ddc":["570"],"file":[{"checksum":"5a455ad914e7d225b1baa4ab07fd925e","success":1,"file_size":278183,"creator":"asandaue","file_id":"9507","content_type":"application/pdf","date_created":"2021-06-07T12:31:36Z","date_updated":"2021-06-07T12:31:36Z","access_level":"open_access","file_name":"2017_GenomeBiology_Zilberman.pdf","relation":"main_file"}],"author":[{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"intvolume":"        18","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"date_created":"2021-06-07T12:27:39Z","status":"public","month":"05","year":"2017","date_published":"2017-05-09T00:00:00Z","department":[{"_id":"DaZi"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation."}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T07:55:02Z","volume":18,"type":"journal_article","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","issue":"1","article_number":"87","citation":{"ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” <i>Genome Biology</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1186/s13059-017-1230-2\">https://doi.org/10.1186/s13059-017-1230-2</a>.","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” <i>Genome Biology</i>, vol. 18, no. 1. Springer Nature, 2017.","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-017-1230-2\">https://doi.org/10.1186/s13059-017-1230-2</a>","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. <i>Genome Biology</i>. 2017;18(1). doi:<a href=\"https://doi.org/10.1186/s13059-017-1230-2\">10.1186/s13059-017-1230-2</a>","short":"D. Zilberman, Genome Biology 18 (2017).","mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” <i>Genome Biology</i>, vol. 18, no. 1, 87, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1186/s13059-017-1230-2\">10.1186/s13059-017-1230-2</a>."},"extern":"1","day":"09","publisher":"Springer Nature","_id":"9506"},{"_id":"9456","article_type":"letter_note","extern":"1","day":"27","publisher":"Springer Nature ","page":"533-536","volume":538,"type":"journal_article","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T07:55:30Z","citation":{"ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>."},"issue":"7626","status":"public","month":"10","year":"2016","author":[{"full_name":"Huff, Jason T.","last_name":"Huff","first_name":"Jason T."},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"full_name":"Roy, Scott W.","first_name":"Scott W.","last_name":"Roy"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"intvolume":"       538","date_created":"2021-06-04T11:34:55Z","department":[{"_id":"DaZi"}],"publication_status":"published","date_published":"2016-10-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}],"article_processing_charge":"No","publication":"Nature","pmid":1,"external_id":{"pmid":["27760113"]},"oa_version":"Submitted Version","doi":"10.1038/nature20110","title":"Mechanism for DNA transposons to generate introns on genomic scales","quality_controlled":"1","scopus_import":"1"},{"article_type":"original","_id":"9473","day":"27","publisher":"National Academy of Sciences","extern":"1","page":"15132-15137","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"journal_article","volume":113,"date_updated":"2023-05-08T11:00:40Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations."}],"citation":{"ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>."},"issue":"52","year":"2016","month":"12","status":"public","date_created":"2021-06-07T06:21:39Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"intvolume":"       113","author":[{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Toby","last_name":"Buttress","full_name":"Buttress, Toby"},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"},{"last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"}],"publication_status":"published","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"date_published":"2016-12-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"article_processing_charge":"No","pmid":1,"publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.1619074114","oa_version":"Published Version","external_id":{"pmid":["27956643"]},"scopus_import":"1","quality_controlled":"1","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues"},{"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_status":"published","date_published":"2016-12-27T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"month":"12","status":"public","year":"2016","intvolume":"       113","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"last_name":"Park","first_name":"Kyunghyuk","full_name":"Park, Kyunghyuk"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"full_name":"Park, Jin-Sup","first_name":"Jin-Sup","last_name":"Park"},{"first_name":"Youbong","last_name":"Hyun","full_name":"Hyun, Youbong"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi"},{"full_name":"Choi, Yeonhee","first_name":"Yeonhee","last_name":"Choi"},{"full_name":"Scholten, Stefan","last_name":"Scholten","first_name":"Stefan"}],"date_created":"2021-06-07T07:10:59Z","oa_version":"Published Version","external_id":{"pmid":["27956642"]},"doi":"10.1073/pnas.1619047114","quality_controlled":"1","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","pmid":1,"page":"15138-15143","_id":"9477","article_type":"original","extern":"1","publisher":"National Academy of Sciences","day":"27","citation":{"short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>."},"issue":"52","volume":113,"type":"journal_article","keyword":["Multidisciplinary"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"date_updated":"2023-05-08T11:00:07Z"},{"publication_status":"published","department":[{"_id":"DaZi"}],"date_published":"2015-12-15T00:00:00Z","year":"2015","status":"public","month":"12","date_created":"2021-06-08T09:56:24Z","author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"intvolume":"        29","file":[{"relation":"main_file","creator":"asandaue","file_id":"9533","content_type":"application/pdf","success":1,"checksum":"086a88cfca4677646da26ed960cb02e9","file_size":1116846,"access_level":"open_access","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","date_updated":"2021-06-08T09:55:10Z","date_created":"2021-06-08T09:55:10Z"}],"oa_version":"Published Version","external_id":{"pmid":["26680300"]},"file_date_updated":"2021-06-08T09:55:10Z","doi":"10.1101/gad.269902.115","ddc":["570"],"scopus_import":"1","title":"Evolution and function of genomic imprinting in plants","quality_controlled":"1","article_processing_charge":"No","publication":"Genes and Development","pmid":1,"page":"2517–2531","_id":"9532","article_type":"review","day":"15","publisher":"Cold Spring Harbor Laboratory Press","extern":"1","citation":{"short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015."},"issue":"24","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"has_accepted_license":"1","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":29,"type":"journal_article","date_updated":"2021-12-14T07:58:15Z","abstract":[{"lang":"eng","text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings."}],"language":[{"iso":"eng"}]},{"extern":"1","publisher":"Elsevier","day":"13","article_type":"original","_id":"9458","page":"1286-1297","language":[{"iso":"eng"}],"abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"date_updated":"2021-12-14T08:22:36Z","volume":156,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"issue":"6","citation":{"apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>"},"intvolume":"       156","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"}],"date_created":"2021-06-04T12:00:16Z","month":"03","status":"public","year":"2014","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"date_published":"2014-03-13T00:00:00Z","department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"publication":"Cell","article_processing_charge":"No","quality_controlled":"1","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","scopus_import":"1","external_id":{"pmid":["24630728"]},"doi":"10.1016/j.cell.2014.01.029","oa_version":"Published Version"},{"article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","pmid":1,"oa_version":"Published Version","external_id":{"pmid":["25344531"]},"doi":"10.1073/pnas.1418564111","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","quality_controlled":"1","scopus_import":"1","status":"public","month":"11","year":"2014","author":[{"last_name":"Mérai","first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna"},{"full_name":"Chumak, Nina","last_name":"Chumak","first_name":"Nina"},{"full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar","first_name":"Marcelina"},{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"full_name":"Schoft, Vera K.","last_name":"Schoft","first_name":"Vera K."},{"full_name":"Bindics, János","first_name":"János","last_name":"Bindics"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"first_name":"Stéphanie","last_name":"Arnoux","full_name":"Arnoux, Stéphanie"},{"last_name":"Opravil","first_name":"Susanne","full_name":"Opravil, Susanne"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"full_name":"Tamaru, Hisashi","first_name":"Hisashi","last_name":"Tamaru"}],"intvolume":"       111","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_created":"2021-06-07T07:23:43Z","department":[{"_id":"DaZi"}],"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"date_published":"2014-11-11T00:00:00Z","type":"journal_article","volume":111,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T08:23:26Z","citation":{"mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171."},"issue":"45","article_type":"original","_id":"9479","extern":"1","publisher":"National Academy of Sciences","day":"11","page":"16166-16171"},{"abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T08:24:48Z","volume":19,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"5","citation":{"mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326."},"extern":"1","day":"04","publisher":"Elsevier","_id":"9519","article_type":"review","page":"320-326","publication":"Trends in Plant Science","pmid":1,"article_processing_charge":"No","title":"DNA methylation as a system of plant genomic immunity","quality_controlled":"1","scopus_import":"1","doi":"10.1016/j.tplants.2014.01.014","oa_version":"None","external_id":{"pmid":["24618094 "]},"author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"intvolume":"        19","publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]},"date_created":"2021-06-07T14:38:09Z","status":"public","month":"05","year":"2014","date_published":"2014-05-04T00:00:00Z","department":[{"_id":"DaZi"}],"publication_status":"published"}]