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| Status |
Public on Nov 19, 2015 |
| Title |
Genome-wide analysis of histone methylations, m5CpG, and SETDB1 binding in ESCs, MSCs, preadipocytes, and adipocytes. |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Bivalent H3K4me3 and H3K27me3 chromatin domains in embryonic stem cells keep active developmental regulatory genes expressed at very low levels and poised for activation. Here, we show an alternative and previously unknown bivalent modified histone signature in lineage-committed mesenchymal stem cells and preadipocytes that pairs H3K4me3 with H3K9me3 to maintain adipogenic master regulatory genes (Cebpa and Pparg) expressed at low levels yet poised for activation when differentiation is required. We show lineage-specific gene-body DNA methylation recruits H3K9 methyltransferase SETDB1 which methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establish the bivalent domain. At the Cebpa locus, this prevents transcription factor C/EBPβ binding, histone acetylation, and further H3K4me3 deposition and is associated with pausing of RNA polymerase II, which limits Cebpa gene expression and adipogenesis.
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| Overall design |
H3K4me3, H3K27me3, H3K9me3, SETDB1, MBD1, and Pol II ChIP-seq. m5CpG pull-down using recombinant MBD domain of MBD1 followed by next-generation sequencing.
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| |
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| Contributor(s) |
Matsumura Y |
| Citation(s) |
26590716 |
| |
| Submission date |
Sep 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoshihiro Matsumura |
| E-mail(s) |
[email protected]
|
| Organization name |
Akita University Graduate School of Medicine
|
| Department |
Biochemistry and Metabolic Science
|
| Street address |
Hondo 1-1-1
|
| City |
Akita |
| State/province |
Akita |
| ZIP/Postal code |
010-8543 |
| Country |
Japan |
| |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (39)
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| This SubSeries is part of SuperSeries: |
| GSE73434 |
H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-specific DNA Methylation Pauses Adipocyte Differentiation |
|
| Relations |
| BioProject |
PRJNA296956 |
| SRA |
SRP064188 |
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