title: Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells.
abstract: Genome-wide distribution of the majority of H2A and H3 variants (H2A, H2AX, H2AZ, macroH2A, H3.1, H3.2 and H3.3) was simultaneously investigated in mouse embryonic stem cells by chromatin immunoprecipitation sequencing. Around the transcription start site, histone variant distribution differed between genes possessing promoters of high and low CpG density, regardless of their expression levels. In the intergenic regions, regulatory elements were enriched in H2A.Z and H3.3, whereas repeat elements were abundant in H2A and macroH2A, and H3.1, respectively. Analysis of H2A and H3 variant combinations composing nucleosomes revealed that the H2A.Z and H3.3 combinations were present at a higher frequency throughout the genome than the other combinations, suggesting that H2A.Z and H3.3 associate preferentially with each other to comprise the nucleosomes independently of genome region. Finally, we found that chromatin was unstable only in regions where it was enriched in both H2A.Z and H3.3, but strongly quantified stable in regions in which only H3.3 was abundant. Therefore, histone variant composition is an important determinant of chromatin structure, which is associated with specific genomic functions.
authors.affiliation: Department of Integrated Biosciences, Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Masashi
authors.initials: M
authors.lastname: Yukawa
authors.affiliation: Department of Integrated Biosciences, Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Tomohiko
authors.initials: T
authors.lastname: Akiyama
authors.affiliation: Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia.
authors.forename: Vedran
authors.initials: V
authors.lastname: Franke
authors.affiliation: Mammalian Cellular Dynamics Team, Bioresource Center, RIKEN Tsukuba Institute, Tsukuba, Japan.
authors.forename: Nathan
authors.initials: N
authors.lastname: Mise
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Isagawa
authors.affiliation: Department of Medical Genome Science, Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Integrated Biosciences, Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Masataka G
authors.initials: MG
authors.lastname: Suzuki
authors.affiliation: Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia.
authors.forename: Kristian
authors.initials: K
authors.lastname: Vlahovicek
authors.affiliation: Mammalian Cellular Dynamics Team, Bioresource Center, RIKEN Tsukuba Institute, Tsukuba, Japan.
authors.forename: Kuniya
authors.initials: K
authors.lastname: Abe
authors.affiliation: Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Aburatani
authors.affiliation: Department of Integrated Biosciences, Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Fugaku
authors.initials: F
authors.lastname: Aoki
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D053595:Embryonic Stem Cells / Q000378:metabolism*; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006657:Histones / Q000235:genetics* / Q000378:metabolism*; D051379:Mice; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional; D012091:Repetitive Sequences, Nucleic Acid; D024363:Transcription Initiation Site
chemical_list: D002843:Chromatin; D006657:Histones