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| Status |
Public on Dec 08, 2015 |
| Title |
Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In mouse embryonic stem cells (mES cells), ubiquitylation of histone H2A lysine 119 represses a large number of developmental genes and maintains mES cell pluripotency. It has been suggested that a number of H2A ubiquitin ligases as well as deubiquitylases and related peptide fragments contribute to a delicate balance between self-renewal and multi-lineage differentiation in mES cells. Here, we tested whether known H2A ubiquitin ligases and deubiquitylases are involved in mES cell regulation and discovered that Dzip3, the E3 ligase of H2AK119, represses differentiation-inducible genes as well as Ring1B. The two sets of target genes partially overlapped but had different spectra. We found that Dzip3 represses gene expression by orchestrating changes in 3D organization in addition to regulating ubiquitylation of H2A. Our results shed light on the epigenetic mechanism of transcriptional regulation, which depends on 3D chromatin reorganization to regulate mES cell differentiation.
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| Overall design |
mouse ES cell mRNA profiles of control, Ring1B knock down, and Dzip3 knock down, in duplicate, using Illumina MiSeq.
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| Contributor(s) |
Inoue D, Ito T |
| Citation(s) |
26568260 |
| Submission date |
Aug 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daishi Inoue |
| Organization name |
Nagasaki univiersity
|
| Department |
medicine
|
| Lab |
Biochemistry
|
| Street address |
Sakamoto
|
| City |
Nagasaki |
| State/province |
1-12-4 |
| ZIP/Postal code |
852-8523 |
| Country |
Japan |
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| Platforms (1) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE71884 |
Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation |
|
| Relations |
| BioProject |
PRJNA292397 |
| SRA |
SRP062216 |
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