Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells

Masashi Yukawa, Tomohiko Akiyama, Vedran Franke, Nathan Mise, Takayuki Isagawa, Yutaka Suzuki, Masataka G. Suzuki, Kristian Vlahovicek, Kuniya Abe, Hiroyuki Aburatani, Fugaku Aoki

Research output: Contribution to journalArticle

13 Citations (Scopus)

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.

Original languageEnglish
Article numbere92689
JournalPloS one
Volume9
Issue number3
DOIs
Publication statusPublished - 2014 Mar 21
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Yukawa, M., Akiyama, T., Franke, V., Mise, N., Isagawa, T., Suzuki, Y., Suzuki, M. G., Vlahovicek, K., Abe, K., Aburatani, H., & Aoki, F. (2014). Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. PloS one, 9(3), [e92689]. https://doi.org/10.1371/journal.pone.0092689