title: High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Benjamin R
authors.initials: BR
authors.lastname: Carone
authors.affiliation: Institute of Bioinformatics and System Biology, National Chiao Tung University, 75 Bo-Ai Street, Hsin-Chu, Taiwan 300; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Jui-Hung
authors.initials: JH
authors.lastname: Hung
authors.affiliation: Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Hainer
authors.affiliation: Institute of Bioinformatics and System Biology, National Chiao Tung University, 75 Bo-Ai Street, Hsin-Chu, Taiwan 300.
authors.forename: Min-Te
authors.initials: MT
authors.lastname: Chou
authors.affiliation: Department of Developmental and Cell Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Carone
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.affiliation: Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Fazzio
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: oliver.rando@umassmed.edu.
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping / Q000379:methods*; D018983:DNA Footprinting; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism*; D008297:Male; D051379:Mice; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D012097:Repressor Proteins / Q000378:metabolism; D013094:Spermatozoa / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D006657:Histones; D009707:Nucleosomes; D012097:Repressor Proteins; D014157:Transcription Factors