TY - JOUR
T1 - Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells
AU - Yukawa, Masashi
AU - Akiyama, Tomohiko
AU - Franke, Vedran
AU - Mise, Nathan
AU - Isagawa, Takayuki
AU - Suzuki, Yutaka
AU - Suzuki, Masataka G.
AU - Vlahovicek, Kristian
AU - Abe, Kuniya
AU - Aburatani, Hiroyuki
AU - Aoki, Fugaku
PY - 2014/3/21
Y1 - 2014/3/21
N2 - 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.
AB - 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.
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U2 - 10.1371/journal.pone.0092689
DO - 10.1371/journal.pone.0092689
M3 - Article
C2 - 24658136
AN - SCOPUS:84899117608
SN - 1932-6203
VL - 9
JO - PLoS One
JF - PLoS One
IS - 3
M1 - e92689
ER -