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Series GSE71882 Query DataSets for GSE71882
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.
Overall design mouse ES cell mRNA profiles of control, Ring1B knock down, and Dzip3 knock down, in duplicate, using Illumina MiSeq.
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
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (6)
GSM1847166 control rep1
GSM1847167 control rep2
GSM1847168 Ring1B-KD rep1
This SubSeries is part of SuperSeries:
GSE71884 Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation
BioProject PRJNA292397
SRA SRP062216

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71882_RAW.tar 640.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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