title: Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping.
abstract: Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. We uncovered surprising features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes, a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that nucleosomes occupy DNA targets for a subset of DNA-binding proteins, including CCCTC-binding factor (CTCF) and pluripotency factors. Furthermore, we provide evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Taken together, we establish an accurate method for defining the nucleosome landscape and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Lilien N
authors.initials: LN
authors.lastname: Voong
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Liqun
authors.initials: L
authors.lastname: Xi
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Amy C
authors.initials: AC
authors.lastname: Sebeson
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Xiong
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208, USA. Electronic address: jzwang@northwestern.edu.
authors.forename: Ji-Ping
authors.initials: JP
authors.lastname: Wang
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA. Electronic address: awang@northwestern.edu.
authors.forename: Xiaozhong
authors.initials: X
authors.lastname: Wang
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D055106:Genome-Wide Association Study; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism*; D009707:Nucleosomes / Q000235:genetics*; D012319:RNA Polymerase II / Q000378:metabolism; D022821:RNA Splice Sites; D012326:RNA Splicing; D012097:Repressor Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D000076246:CCCTC-Binding Factor; C000619698:Ctcf protein, mouse; D009707:Nucleosomes; D022821:RNA Splice Sites; D012097:Repressor Proteins; D012319:RNA Polymerase II
keywords: CTCF; MNase; chemical biology; chromatin; embryonic stem cells; epigenetics; nucleosomes; pioneer transcription factors; pluripotency; splicing