Transcriptomics

Dataset Information

297

H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs [RNA-Seq]


ABSTRACT: The H2A variant H2AZ is essential for embryonic development and for proper execution of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions in H2AZ are likely key for its functional specialization, but we know little about how these differences contribute to chromatin regulation. Here, we show that the extended acidic patch, specifically the three divergent residues in the C-terminal docking domain, is necessary for lineage commitment during ESC differentiation and proper execution of gene expression programs during ESC differentiation. Surprisingly, disruption of the acidic patch domain has a distinct consequence on cellular specification compared to H2AZ depletion. This is consistent with differences in gene expression profiles of H2AZ –depleted and acidic patch (AP) mutant ESCs during early lineage commitment. Interestingly, the distinct consequence of AP mutant expression on gene regulation is coincidence with an altered destabilized chromatin state and high chromatin mobility dependent on active transcription. Collectively, our data shows that the divergent residues within the acidic patch domain are key structural determinants of H2AZ function and links chromatin structure and dynamics with gene regulation and cell fate specification. H2AZ extended acidic patch was mutated, or H2AZ was KD in mouse embryonic stem cells and RNA-Seq analysis was performed on the resulting cultures. Characterization of H2AZ-WT and -AP3-mutant binding specificities were performed by ChIP-Seq.

ORGANISM(S): Mus musculus  

SUBMITTER: Laurie A Boyer   Vidya Subramanian 

PROVIDER: E-GEOD-40064 | ArrayExpress | 2013-09-23

SECONDARY ACCESSION(S): GSE40064SRP014791PRJNA172651

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation.

Subramanian Vidya V   Mazumder Aprotim A   Surface Lauren E LE   Butty Vincent L VL   Fields Paul A PA   Alwan Allison A   Torrey Lillian L   Thai Kevin K KK   Levine Stuart S SS   Bathe Mark M   Boyer Laurie A LA  

PLoS genetics 20130822 8


The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For example, H2A.Z contains three divergent residues in the essential C-terminal acidic patch that reside on the surface of the histone octamer as an uninterrupted acidic patch domain; however, we know littl  ...[more]

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