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Series GSE40063 Query DataSets for GSE40063
Status Public on Sep 23, 2013
Title H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design 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.
Contributor(s) Subramanian V, Boyer LA
Citation(s) 23990805
Submission date Aug 13, 2012
Last update date May 15, 2019
Contact name Laurie A Boyer
Phone 617 324-3335
Organization name Massachusetts Institute of Technology
Department Biology
Lab Boyer
Street address 77 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (3)
GSM984544 H2AZ WT ChIP-Seq
GSM984545 H2AZ-AP3-modified ChIP-Seq
GSM984546 H3K27me3 ChIP-Seq
This SubSeries is part of SuperSeries:
GSE40065 H2AZ extended acidic patch is necessary for formation specialized chromatin states in ESCs
BioProject PRJNA172650
SRA SRP014793

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Supplementary file Size Download File type/resource
GSE40063_RAW.tar 507.5 Mb (http)(custom) TAR (of BED, BIGWIG)
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Processed data provided as supplementary file
Raw data are available in SRA

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