Show simple item record

dc.contributor.authorvan der Velde, Arjan
dc.contributor.authorFan, Kaili
dc.contributor.authorTsuji, Junko
dc.contributor.authorMoore, Jill E.
dc.contributor.authorPurcaro, Michael J.
dc.contributor.authorPratt, Henry E
dc.contributor.authorWeng, Zhiping
dc.date2022-08-11T08:09:59.000
dc.date.accessioned2022-08-23T16:51:05Z
dc.date.available2022-08-23T16:51:05Z
dc.date.issued2021-02-22
dc.date.submitted2021-05-05
dc.identifier.citation<p>van der Velde A, Fan K, Tsuji J, Moore JE, Purcaro MJ, Pratt HE, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Commun Biol. 2021 Feb 22;4(1):239. doi: 10.1038/s42003-021-01756-4. PMID: 33619351; PMCID: PMC7900196. <a href="https://doi.org/10.1038/s42003-021-01756-4">Link to article on publisher's site</a></p>
dc.identifier.issn2399-3642 (Linking)
dc.identifier.doi10.1038/s42003-021-01756-4
dc.identifier.pmid33619351
dc.identifier.urihttp://hdl.handle.net/20.500.14038/41791
dc.description.abstractThe morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. This collection of chromatin state assignments provides a useful resource for studying mammalian development.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=33619351&dopt=Abstract">Link to Article in PubMed</a></p>
dc.rightsCopyright © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectEpigenetic memory
dc.subjectGenome informatics
dc.subjectEpigenomics
dc.subjectGene regulation
dc.subjectCell Biology
dc.subjectDevelopmental Biology
dc.subjectGenomics
dc.subjectIntegrative Biology
dc.titleAnnotation of chromatin states in 66 complete mouse epigenomes during development
dc.typeJournal Article
dc.source.journaltitleCommunications biology
dc.source.volume4
dc.source.issue1
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=5623&amp;context=oapubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/4591
dc.identifier.contextkey22797289
refterms.dateFOA2022-08-23T16:51:05Z
html.description.abstract<p>The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. This collection of chromatin state assignments provides a useful resource for studying mammalian development.</p>
dc.identifier.submissionpathoapubs/4591
dc.contributor.departmentGraduate School of Biomedical Sciences
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.source.pages239


Files in this item

Thumbnail
Name:
s42003_021_01756_4.pdf
Size:
22.57Mb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record

Copyright © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Except where otherwise noted, this item's license is described as Copyright © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.