[{"external_id":{"pmid":["36639687"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-08T10:52:49Z","publication_identifier":{"issn":["1474-760X"]},"article_type":"original","year":"2023","oa_version":"Published Version","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"oa":1,"volume":24,"article_processing_charge":"No","article_number":"7","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"_id":"12668","date_published":"2023-01-13T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1186/s13059-022-02844-2","citation":{"ieee":"L. Zhao <i>et al.</i>, “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” <i>Genome Biology</i>, vol. 24. Springer Nature, 2023.","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>.","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>, vol. 24, 7, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. 2023;24. doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>"},"title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","day":"13","author":[{"last_name":"Zhao","full_name":"Zhao, Long","first_name":"Long"},{"last_name":"Yang","full_name":"Yang, Yiman","first_name":"Yiman"},{"last_name":"Chen","first_name":"Jinchao","full_name":"Chen, Jinchao"},{"last_name":"Lin","first_name":"Xuelei","full_name":"Lin, Xuelei"},{"last_name":"Zhang","first_name":"Hao","full_name":"Zhang, Hao"},{"full_name":"Wang, Hao","first_name":"Hao","last_name":"Wang"},{"last_name":"Wang","full_name":"Wang, Hongzhe","first_name":"Hongzhe"},{"last_name":"Bie","first_name":"Xiaomin","full_name":"Bie, Xiaomin"},{"last_name":"Jiang","first_name":"Jiafu","full_name":"Jiang, Jiafu"},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234"},{"full_name":"Fu, Xiangdong","first_name":"Xiangdong","last_name":"Fu"},{"last_name":"Zhang","full_name":"Zhang, Xiansheng","first_name":"Xiansheng"},{"first_name":"Zhuo","full_name":"Du, Zhuo","last_name":"Du"},{"last_name":"Xiao","full_name":"Xiao, Jun","first_name":"Jun"}],"type":"journal_article","publisher":"Springer Nature","publication":"Genome Biology","department":[{"_id":"XiFe"}],"quality_controlled":"1","status":"public","intvolume":"        24","month":"01","extern":"1","date_created":"2023-02-23T09:13:49Z"},{"author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","first_name":"Victoria","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva"},{"last_name":"Diez","full_name":"Diez, Aránzazu Rosado","first_name":"Aránzazu Rosado"},{"last_name":"Espinar","first_name":"Lorena","full_name":"Espinar, Lorena"},{"full_name":"Pérez, Albert Torelló","first_name":"Albert Torelló","last_name":"Pérez"},{"last_name":"Filion","full_name":"Filion, Guillaume J.","first_name":"Guillaume J."}],"type":"journal_article","day":"12","title":"Strand asymmetry influences mismatch resolution during single-strand annealing","citation":{"ama":"Pokusaeva V, Diez AR, Espinar L, Pérez AT, Filion GJ. Strand asymmetry influences mismatch resolution during single-strand annealing. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02665-3\">10.1186/s13059-022-02665-3</a>","apa":"Pokusaeva, V., Diez, A. R., Espinar, L., Pérez, A. T., &#38; Filion, G. J. (2022). Strand asymmetry influences mismatch resolution during single-strand annealing. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-022-02665-3\">https://doi.org/10.1186/s13059-022-02665-3</a>","short":"V. Pokusaeva, A.R. Diez, L. Espinar, A.T. Pérez, G.J. Filion, Genome Biology 23 (2022).","mla":"Pokusaeva, Victoria, et al. “Strand Asymmetry Influences Mismatch Resolution during Single-Strand Annealing.” <i>Genome Biology</i>, vol. 23, 93, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02665-3\">10.1186/s13059-022-02665-3</a>.","chicago":"Pokusaeva, Victoria, Aránzazu Rosado Diez, Lorena Espinar, Albert Torelló Pérez, and Guillaume J. Filion. “Strand Asymmetry Influences Mismatch Resolution during Single-Strand Annealing.” <i>Genome Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02665-3\">https://doi.org/10.1186/s13059-022-02665-3</a>.","ieee":"V. Pokusaeva, A. R. Diez, L. Espinar, A. T. Pérez, and G. J. Filion, “Strand asymmetry influences mismatch resolution during single-strand annealing,” <i>Genome Biology</i>, vol. 23. Springer Nature, 2022.","ista":"Pokusaeva V, Diez AR, Espinar L, Pérez AT, Filion GJ. 2022. Strand asymmetry influences mismatch resolution during single-strand annealing. Genome Biology. 23, 93."},"ec_funded":1,"doi":"10.1186/s13059-022-02665-3","ddc":["570"],"language":[{"iso":"eng"}],"pmid":1,"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"related_material":{"link":[{"url":"https://github.com/cellcomplexitylab/strand_asymmetry ","relation":"software"},{"relation":"software","url":"https://hub.docker.com/r/gui11aume/strand_asymmetry"}]},"acknowledgement":"We acknowledge the financial support of the Natural Sciences and Engineering Research Council of Canada (NSERC RGPIN-2020-06377), the Spanish Ministry of Economy, Industry and Competitiveness (“Centro de Excelencia Severo Ochoa 2013-2017”, Plan Estatal PGC2018-099807-B-I00), of the CERCA Programme/Generalitat de Catalunya, and of the European Research Council (Synergy Grant 609989). VOP was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385). We also acknowledge the support of the Spanish Ministry of Economy and Competitiveness (MEIC) to the EMBL partnership.","date_created":"2023-01-16T09:48:44Z","month":"04","status":"public","intvolume":"        23","publication":"Genome Biology","quality_controlled":"1","department":[{"_id":"MaJö"}],"isi":1,"publisher":"Springer Nature","year":"2022","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["1474-760X"]},"scopus_import":"1","external_id":{"pmid":["35414014"],"isi":["000781953800001"]},"date_updated":"2023-08-04T09:27:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-04-12T00:00:00Z","_id":"12226","abstract":[{"lang":"eng","text":"Background: Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contributions of DNA repair from those of DNA damage.\r\n\r\nResults: Here, we develop a genome-wide assay whereby the same DNA lesion is repaired in different genomic contexts. We insert thousands of barcoded transposons carrying a reporter of DNA mismatch repair in the genome of mouse embryonic stem cells. Upon inducing a double-strand break between tandem repeats, a mismatch is generated if the break is repaired through single-strand annealing. The resolution of the mismatch showed a 60–80% bias in favor of the strand with the longest 3′ flap. The location of the lesion in the genome and the type of mismatch had little influence on the bias. Instead, we observe a complete reversal of the bias when the longest 3′ flap is moved to the opposite strand by changing the position of the double-strand break in the reporter.\r\n\r\nConclusions: These results suggest that the processing of the double-strand break has a major influence on the repair of mismatches during single-strand annealing."}],"article_number":"93","file":[{"date_updated":"2023-01-27T09:01:40Z","access_level":"open_access","checksum":"17bb091fec04d82ba20a3458c4cfd2bd","file_name":"2022_GenomeBiology_Pokusaeva.pdf","creator":"dernst","file_size":4939342,"success":1,"date_created":"2023-01-27T09:01:40Z","content_type":"application/pdf","file_id":"12419","relation":"main_file"}],"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":23,"file_date_updated":"2023-01-27T09:01:40Z","oa":1,"publication_status":"published"},{"article_number":"221","_id":"11064","abstract":[{"lang":"eng","text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients."}],"date_published":"2018-12-20T00:00:00Z","article_processing_charge":"No","volume":19,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-018-1599-6"}],"oa":1,"article_type":"original","oa_version":"Published Version","year":"2018","external_id":{"pmid":["30567591"]},"scopus_import":"1","date_updated":"2022-07-18T08:32:34Z","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","publication_identifier":{"issn":["1474-760X"]},"month":"12","extern":"1","date_created":"2022-04-07T07:45:40Z","publication":"Genome Biology","quality_controlled":"1","intvolume":"        19","status":"public","publisher":"BioMed Central","day":"20","author":[{"last_name":"Fleischer","full_name":"Fleischer, Jason G.","first_name":"Jason G."},{"last_name":"Schulte","full_name":"Schulte, Roberta","first_name":"Roberta"},{"first_name":"Hsiao H.","full_name":"Tsai, Hsiao H.","last_name":"Tsai"},{"full_name":"Tyagi, Swati","first_name":"Swati","last_name":"Tyagi"},{"first_name":"Arkaitz","full_name":"Ibarra, Arkaitz","last_name":"Ibarra"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"last_name":"Navlakha","full_name":"Navlakha, Saket","first_name":"Saket"}],"type":"journal_article","citation":{"short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1599-6\">10.1186/s13059-018-1599-6</a>","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1599-6\">https://doi.org/10.1186/s13059-018-1599-6</a>","chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1599-6\">https://doi.org/10.1186/s13059-018-1599-6</a>.","ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221.","ieee":"J. G. Fleischer <i>et al.</i>, “Predicting age from the transcriptome of human dermal fibroblasts,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” <i>Genome Biology</i>, vol. 19, 221, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1599-6\">10.1186/s13059-018-1599-6</a>."},"title":"Predicting age from the transcriptome of human dermal fibroblasts","language":[{"iso":"eng"}],"doi":"10.1186/s13059-018-1599-6","pmid":1},{"doi":"10.1186/s13059-017-1230-2","ddc":["570"],"language":[{"iso":"eng"}],"pmid":1,"author":[{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"type":"journal_article","day":"09","title":"An evolutionary case for functional gene body methylation in plants and animals","citation":{"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>.","ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","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.","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>."},"intvolume":"        18","status":"public","publication":"Genome Biology","department":[{"_id":"DaZi"}],"quality_controlled":"1","publisher":"Springer Nature","date_created":"2021-06-07T12:27:39Z","month":"05","extern":"1","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"scopus_import":"1","external_id":{"pmid":["28486944"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T07:55:02Z","has_accepted_license":"1","oa_version":"Published Version","year":"2017","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":18,"file_date_updated":"2021-06-07T12:31:36Z","oa":1,"publication_status":"published","abstract":[{"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.","lang":"eng"}],"_id":"9506","date_published":"2017-05-09T00:00:00Z","article_number":"87","file":[{"checksum":"5a455ad914e7d225b1baa4ab07fd925e","access_level":"open_access","date_updated":"2021-06-07T12:31:36Z","creator":"asandaue","file_size":278183,"file_name":"2017_GenomeBiology_Zilberman.pdf","date_created":"2021-06-07T12:31:36Z","success":1,"file_id":"9507","relation":"main_file","content_type":"application/pdf"}],"article_processing_charge":"No","issue":"1"},{"publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T09:09:41Z","scopus_import":"1","external_id":{"pmid":["16277745"]},"oa_version":"Published Version","year":"2005","article_type":"original","volume":6,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/gb-2005-6-11-r90"}],"publication_status":"published","_id":"9514","date_published":"2005-10-19T00:00:00Z","abstract":[{"text":"Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.","lang":"eng"}],"article_number":"R90","issue":"11","article_processing_charge":"No","doi":"10.1186/gb-2005-6-11-r90","language":[{"iso":"eng"}],"pmid":1,"author":[{"full_name":"Tran, Robert K.","first_name":"Robert K.","last_name":"Tran"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"first_name":"Cecilia","full_name":"de Bustos, Cecilia","last_name":"de Bustos"},{"first_name":"Renata F.","full_name":"Ditt, Renata F.","last_name":"Ditt"},{"last_name":"Henikoff","full_name":"Henikoff, Jorja G.","first_name":"Jorja G."},{"last_name":"Lindroth","full_name":"Lindroth, Anders M.","first_name":"Anders M."},{"last_name":"Delrow","first_name":"Jeffrey","full_name":"Delrow, Jeffrey"},{"full_name":"Boyle, Tom","first_name":"Tom","last_name":"Boyle"},{"last_name":"Kwong","full_name":"Kwong, Samson","first_name":"Samson"},{"full_name":"Bryson, Terri D.","first_name":"Terri D.","last_name":"Bryson"},{"last_name":"Jacobsen","full_name":"Jacobsen, Steven E.","first_name":"Steven E."},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"}],"type":"journal_article","day":"19","title":"Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis","citation":{"chicago":"Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>. Springer Nature, 2005. <a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">https://doi.org/10.1186/gb-2005-6-11-r90</a>.","ista":"Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), R90.","ieee":"R. K. Tran <i>et al.</i>, “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” <i>Genome Biology</i>, vol. 6, no. 11. Springer Nature, 2005.","mla":"Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>, vol. 6, no. 11, R90, Springer Nature, 2005, doi:<a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">10.1186/gb-2005-6-11-r90</a>.","short":"R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005).","ama":"Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>. 2005;6(11). doi:<a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">10.1186/gb-2005-6-11-r90</a>","apa":"Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">https://doi.org/10.1186/gb-2005-6-11-r90</a>"},"status":"public","intvolume":"         6","quality_controlled":"1","department":[{"_id":"DaZi"}],"publication":"Genome Biology","publisher":"Springer Nature","date_created":"2021-06-07T13:12:41Z","extern":"1","month":"10"},{"year":"2004","oa_version":"Published Version","article_type":"review","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"scopus_import":"1","external_id":{"pmid":["15575975"]},"date_updated":"2021-12-14T08:44:24Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","issue":"12","date_published":"2004-11-16T00:00:00Z","_id":"9511","abstract":[{"lang":"eng","text":"Recent progress in understanding the silencing of transposable elements in the model plant Arabidopsis has revealed an interplay between DNA methylation, histone methylation and small interfering RNAs. DNA and histone methylation are not always sufficient to maintain silencing, and RNA-based reinforcement can be needed to maintain as well as initiate it."}],"article_number":"249","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/gb-2004-5-12-249"}],"oa":1,"publication_status":"published","volume":5,"title":"Silencing of transposons in plant genomes: kick them when they're down","citation":{"short":"D. Zilberman, S. Henikoff, Genome Biology 5 (2004).","apa":"Zilberman, D., &#38; Henikoff, S. (2004). Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>","ama":"Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them when they’re down. <i>Genome Biology</i>. 2004;5(12). doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>","ista":"Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes: kick them when they’re down. Genome Biology. 5(12), 249.","ieee":"D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes: kick them when they’re down,” <i>Genome Biology</i>, vol. 5, no. 12. Springer Nature, 2004.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">https://doi.org/10.1186/gb-2004-5-12-249</a>.","mla":"Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant Genomes: Kick Them When They’re Down.” <i>Genome Biology</i>, vol. 5, no. 12, 249, Springer Nature, 2004, doi:<a href=\"https://doi.org/10.1186/gb-2004-5-12-249\">10.1186/gb-2004-5-12-249</a>."},"author":[{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"}],"type":"journal_article","day":"16","pmid":1,"doi":"10.1186/gb-2004-5-12-249","language":[{"iso":"eng"}],"date_created":"2021-06-07T12:58:06Z","month":"11","extern":"1","publisher":"Springer Nature","status":"public","intvolume":"         5","publication":"Genome Biology","department":[{"_id":"DaZi"}],"quality_controlled":"1"}]