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Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation.

Inoue D, Aihara H, Sato T, Mizusaki H, Doiguchi M, Higashi M, Imamura Y, Yoneda M, Miyanishi T, Fujii S, Okuda A, Nakagawa T, Ito T - Sci Rep (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Nagasaki University School of Medicine.

ABSTRACT
In mouse embryonic stem (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 does 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.

No MeSH data available.


Developmental genes are regulated by Ring1B, Dzip3, and H2A ubiquitylation.(A) Venn diagram representing the overlap between genes having Dzip3 peaks around the transcription start site (TSS) by ChIP-seq analysis and upregulated genes in Dzip3 KD cells by RNA-seq analysis. The number in the overlapped region represents the total number of genes exhibiting both. (B) Gene ontology (GO) analysis of Dzip3 target genes. (C) Left panel: ChIP-seq signal profiles of Dzip3, Ring1B, and ubH2A around the promoter region. Right panel: ChIP-qPCR analysis of the promoter region for negative control (NC), Ring1B KD, and Dzip3 KD mES cells. Statistical significance was assessed using a two-tailed Student’s t-test. Error bars, standard deviation.
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f3: Developmental genes are regulated by Ring1B, Dzip3, and H2A ubiquitylation.(A) Venn diagram representing the overlap between genes having Dzip3 peaks around the transcription start site (TSS) by ChIP-seq analysis and upregulated genes in Dzip3 KD cells by RNA-seq analysis. The number in the overlapped region represents the total number of genes exhibiting both. (B) Gene ontology (GO) analysis of Dzip3 target genes. (C) Left panel: ChIP-seq signal profiles of Dzip3, Ring1B, and ubH2A around the promoter region. Right panel: ChIP-qPCR analysis of the promoter region for negative control (NC), Ring1B KD, and Dzip3 KD mES cells. Statistical significance was assessed using a two-tailed Student’s t-test. Error bars, standard deviation.

Mentions: To determine the genome-wide locations of Dzip3 and Ring1B binding sites and the positions of ubH2A modification in a genome-wide manner, we performed ChIP-seq with anti-Dzip3, anti-Ring1B, and anti-ubH2A antibodies under pluripotent conditions (2i + LIF). A Venn diagram was used to represent the 92 genes that overlapped between the set of genes bound by Dzip3 around their transcription start sites (TSS) and the set of genes upregulated by Dzip3 KD (Fig. 3A).


Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation.

Inoue D, Aihara H, Sato T, Mizusaki H, Doiguchi M, Higashi M, Imamura Y, Yoneda M, Miyanishi T, Fujii S, Okuda A, Nakagawa T, Ito T - Sci Rep (2015)

Developmental genes are regulated by Ring1B, Dzip3, and H2A ubiquitylation.(A) Venn diagram representing the overlap between genes having Dzip3 peaks around the transcription start site (TSS) by ChIP-seq analysis and upregulated genes in Dzip3 KD cells by RNA-seq analysis. The number in the overlapped region represents the total number of genes exhibiting both. (B) Gene ontology (GO) analysis of Dzip3 target genes. (C) Left panel: ChIP-seq signal profiles of Dzip3, Ring1B, and ubH2A around the promoter region. Right panel: ChIP-qPCR analysis of the promoter region for negative control (NC), Ring1B KD, and Dzip3 KD mES cells. Statistical significance was assessed using a two-tailed Student’s t-test. Error bars, standard deviation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4645096&req=5

f3: Developmental genes are regulated by Ring1B, Dzip3, and H2A ubiquitylation.(A) Venn diagram representing the overlap between genes having Dzip3 peaks around the transcription start site (TSS) by ChIP-seq analysis and upregulated genes in Dzip3 KD cells by RNA-seq analysis. The number in the overlapped region represents the total number of genes exhibiting both. (B) Gene ontology (GO) analysis of Dzip3 target genes. (C) Left panel: ChIP-seq signal profiles of Dzip3, Ring1B, and ubH2A around the promoter region. Right panel: ChIP-qPCR analysis of the promoter region for negative control (NC), Ring1B KD, and Dzip3 KD mES cells. Statistical significance was assessed using a two-tailed Student’s t-test. Error bars, standard deviation.
Mentions: To determine the genome-wide locations of Dzip3 and Ring1B binding sites and the positions of ubH2A modification in a genome-wide manner, we performed ChIP-seq with anti-Dzip3, anti-Ring1B, and anti-ubH2A antibodies under pluripotent conditions (2i + LIF). A Venn diagram was used to represent the 92 genes that overlapped between the set of genes bound by Dzip3 around their transcription start sites (TSS) and the set of genes upregulated by Dzip3 KD (Fig. 3A).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Nagasaki University School of Medicine.

ABSTRACT
In mouse embryonic stem (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 does 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.

No MeSH data available.