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Genome-wide maps of the H3K27me3 histone modification in wild-type or SUZ12-mutant ipNF05.5 cells.

ABSTRACT: Using ChIP-seq, we profiled the H3K27me3 histone mark in wild-type or SUZ12-mutant ipNF05.5 cells.

OTHER RELATED OMICS DATASETS IN: PXD012547

ORGANISM(S): Homo sapiens

PROVIDER: GSE118183 | GEO | 2019/03/03

REPOSITORIES: GEO

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Genome-wide maps of the H3K27me3 histone modification in wild-type or SUZ12-mutant ipNF05.5 cells.

Project description:Genome-wide maps of the H3K27me3 histone modification in wild-type or SUZ12-mutant ipNF05.5 cells.

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Project description:We investigate the contribution of each SUZ12 isoform on PRC2 activity on chromatin using our different ESC lines. As an additional comparison for ∆ex4 cells (SUZ12-S), we included an ESC clone in which an unsuccessful CRISPR editing event resulted in a mutant allele with nearly constitutive splicing of exon 4 (herein, CSex4) and normal Suz12 expression levels (expressing only SUZ12-L). First, we profiled H3K27 bulk PTMs by WB and observed that, while CSex4 cells showed no major differences to control cells, ∆ex4 cells displayed lower levels of H3K27me2 and -me3, with higher levels of mono-methylation and acetylation. Similar results were obtained when comparing SUZ12-L and SUZ12-S ESC rescue lines. To validate these findings with an antibody-independent technique, and to additionally profile other histone PTMs, we analysed these cells with histone-MS. In line with the previous estimates26, WT cells displayed approximately 85% of H3K27 methylation. This proportion was largely similar in CSex4 cells, while it dropped to ~50% in ∆ex4 cells, with H3K27me2 and -me3 being the most affected modifications. Notably, H3K27me2/3 loss in ∆ex4 cells occurred at histone peptides regardless of their H3K36 methylation status. Moreover, the global H3K36 methylation rates were not affected in either CSex4 or ∆ex4 cells (Figure S4C), and no major changes in methylation or acetylation levels were observed at other residues. Importantly, reintroduction of SUZ12-L in KO cells rescued a higher degree of methylation compared to SUZ12-S. Overall, these results indicate that SUZ12-S alone is unable to maintain global physiological levels of H3K27 methylation; rather SUZ12-L is also necessary for this task.

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