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dc.contributor.authorCarone, Benjamin R.
dc.contributor.authorHung, Jui-Hung
dc.contributor.authorHainer, Sarah J.
dc.contributor.authorChou, Min-Te
dc.contributor.authorCarone, Dawn M.
dc.contributor.authorWeng, Zhiping
dc.contributor.authorFazzio, Thomas G.
dc.contributor.authorRando, Oliver J.
dc.date2022-08-11T08:10:15.000
dc.date.accessioned2022-08-23T17:01:35Z
dc.date.available2022-08-23T17:01:35Z
dc.date.issued2014-07-14
dc.date.submitted2014-08-22
dc.identifier.citationCarone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell. 2014 Jul 14;30(1):11-22. doi: 10.1016/j.devcel.2014.05.024. <a href="http://dx.doi.org/10.1016/j.devcel.2014.05.024">Link to article on publisher's site</a>
dc.identifier.issn1534-5807 (Linking)
dc.identifier.doi10.1016/j.devcel.2014.05.024
dc.identifier.pmid24998598
dc.identifier.urihttp://hdl.handle.net/20.500.14038/44041
dc.description.abstractMammalian embryonic stem cells (ESCs) and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ESCs and sperm. In ESCs, we recover well-characterized features of chromatin such as promoter nucleosome depletion and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ESCs and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome.
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=24998598&dopt=Abstract">Link to Article in PubMed</a>
dc.relation.urlhttp://dx.doi.org/10.1016/j.devcel.2014.05.024
dc.subjectBioinformatics
dc.subjectCell Biology
dc.subjectComputational Biology
dc.subjectDevelopmental Biology
dc.subjectGenetics and Genomics
dc.subjectIntegrative Biology
dc.titleHigh-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm
dc.typeJournal Article
dc.source.journaltitleDevelopmental cell
dc.source.volume30
dc.source.issue1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/pgfe_pp/256
dc.identifier.contextkey6022382
html.description.abstract<p>Mammalian embryonic stem cells (ESCs) and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ESCs and sperm. In ESCs, we recover well-characterized features of chromatin such as promoter nucleosome depletion and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ESCs and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome.</p>
dc.identifier.submissionpathpgfe_pp/256
dc.contributor.departmentDepartment of Developmental and Cell Biology
dc.contributor.departmentProgram in Gene Function and Expression
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.source.pages11-22


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