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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Daishi Inoue

PROVIDER: E-GEOD-71884 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Inoue Daishi D Aihara Hitoshi H Sato Tatsuharu T Mizusaki Hirofumi H Doiguchi Masamichi M Higashi Miki M Imamura Yuko Y Yoneda Mitsuhiro M Miyanishi Takayuki T Fujii Satoshi S Okuda Akihiko A Nakagawa Takeya T Ito Takashi T

Scientific reports 20151116

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 disco ...[more]

PMID: 26568260

Similar Datasets

Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation [ChIP-seq]

Project description: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 hadãdifferent 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. Examination of 3 different histone modifications in 1 cell type.

2015-12-08 | E-GEOD-71883 | biostudies-arrayexpress

Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation [RNA-seq]

Project description: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. mouse ES cell mRNA profiles of control, Ring1B knock down, and Dzip3 knock down, in duplicate, using Illumina MiSeq.

2015-12-08 | E-GEOD-71882 | biostudies-arrayexpress

ChIP-seq of RNA polymerase II using pan-pol II and S2-phosphorylated C-terminal domain antibodies in mouse embryonic stem cells

Project description:Our proteomics data (PXD030253) indicate RNA polymerase II is co-localized with Aldh18a1. To confirm this observation using an orthogonal method we performed ChIP-seq experiments to identify the binding patterns of RNA polymerase II in general, and RNA polymerase II with S2-phosphorylated CTD. We also performed Cut&Run using Aldh18a1 antibody which is submitted separately. To do a ChIP-seq, mES cells (46C) were treated with Accutase to be detached. The cells were fixed by 1.5% formaldehyde in PBS for 15min. Chromatin was fragmented by sonication and sheared to < 500 bp fragments. The cell debris were removed by spinning. The sheared chromatin was treated with 10 ug antibodies (pan-Pol II Bethyl A304-405A, or S2P-Pol II Bethyl A304-407A) overnight at 4 °C. Dynabeads protein A beads (40ul) were added to the samples and the samples were rotated 2-3 hours to perform the immunoprecipitation. The beads were washed 5 times. Chromatin was eluted in a denaturing solution, and proteins were digested using proteinase K. DNA was purified by SPRI beads. The ChIP libraries were prepared using NEBNext Ultra II DNA library prep according to the manufacturer manual. The libraries were sequenced using 150nt reads on paired-end mode by HiSeq4000. Reads were trimmed, aligned to the mouse genome (mm10) using Bowtie2, and duplicated reads were removed with samtools. The ChIP quality was evaluated by cross-correlation using the “SPP'' tool as suggested by ENCODE ChIP-seq guidelines. Peak calling was performed using MACS2.

2022-06-01 | E-MTAB-11510 | biostudies-arrayexpress

Deciphering the relationship between polycomb repression and stochastic gene expression from single-cell RNA-seq data

Project description:Polycomb repressive complexes are important histone modifiers, which silence gene expression, yet there exists a subset of polycomb-bound genes actively transcribed by RNA polymerase II. To investigate the switching between polycomb-repressed and active states, we sequence mRNA from OS25 mouse embryonic stem cells cultured in serum/LIF. To validate our finding that polycomb modulates stochastic gene expression and transcriptional bursting, we perform knockout experiments and we sequence mRNA from Ring1A knockout (untreated) and Ring1A/B double knockout cells with constitutive Ring1A knockout and tamoxifen-inducible conditional Ring1B knockout.

2017-06-01 | E-MTAB-5661 | biostudies-arrayexpress

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-05-18 | E-GEOD-66526 | biostudies-arrayexpress

Investigation of the role of histone modification propagating activity of GLP

Project description:We use ChIP-Seq and RNA-Seq technology to profile the H3K9me2 modification and transcription under different conditions of GLP activity. GLP and G9a are major H3K9 dimethylases, and are essential for mouse early embryonic development. Here we report that GLP and G9a possess intrinsic histone methylation propagating activities. The histone methyltransferase activities of GLP and G9a are stimulated by neighboring nucleosomes pre-methylated at H3K9. These stimulation events function in cis and are dependent on H3K9 methylation binding activities of ankyrin repeats domains in GLP and G9a. In mouse embryonic stem cells (ESCs) harboring a mutant GLP lacking H3K9 methylation propagating activity, pluripotent genes display a delayed kinetics in establishing H3K9 methylation and gene silencing during differentiation. Disruption of the H3K9 methylation propagating activity of GLP in mice causes growth retardation of the embryos, ossification defects of calvaria and early postnatal lethality. We propose that GLP¡¯s ability to rapidly propagate H3K9 methylation is required for efficient gene silencing during programmed cell fate transition. H3K9me2 and H3K9me1 are ChIPped and sequenced in WT mESC and GLP-mutant mESCs, and RNA-Seq was done for those cells as well.

2015-01-20 | E-GEOD-54412 | biostudies-arrayexpress

The Polycomb protein Pcgf2/Mel18 regulates mesoderm cell fate-specification of embryonic stem cells through multiple mechanisms

Project description:Polycomb complexes are essential regulators of stem cell identity, yet very little is known about their molecular mechanisms during cell differentiation. Pcgf proteins (Pcgf1/2/3/4/5/6) are core subunits of the Polycomb repressive complex 1 (PRC1). It has been recently proposed that specific Pcgf proteins are associated to particular PRC1 complexes, yet the molecular and biological functions of different Pcgf proteins remains largely elusive. Using specific differentiation protocols, we have elucidated a role for Pcgf2/Mel18 in specifically regulating mesoderm differentiation. Mechanistically, during early cardiac mesoderm differentiation, Pcgf2/Mel18 functions as a classical Polycomb protein by repressing pluripotency, lineage specification, late cardiac differentiation and negative regulators of the BMP pathway, yet Pcgf2/Mel18 also positively regulates the expression of key mesoderm transcription factors, revealing a novel function of Pcgf2/Mel18 in gene activation during cardiac differentiation. Mel18 depletion results in an unbalance of pathways that positively and negatively regulate cardiac differentiation. We propose that Mel18 is a novel epigenetic factor that controls mesoderm differentiation by opposing molecular mechanisms. List of ChIPseq samples: Mel18 in ESCs and MES, Ring1b, RYBP and Cbx2 in MES, IgG in MESs. List of RNAseq experiments: Mel18 KD, Ring1b KO and CTR in ESCs, Mel18 KD and CTR in MES, Mel18 KD and CTR in CMs.

2015-09-04 | E-GEOD-67868 | biostudies-arrayexpress

ETO Family Protein Mtgr1 Mediates Prdm14 Functions in Stem Cell Maintenance

Project description:Prdm14 is a sequence-specific transcriptional regulator of embryonic stem cell (ESC) pluripotency and primordial germ cell (PGC) formation. It exerts its function, at least in part, through repressing genes associated with epigenetic modification and cell differentiation. Here, we show that this repressive function is mediated through an ETO-family co-repressor Mtgr1, which tightly binds to the pre-SET/SET domains of Prdm14 and co-occupies its genomic targets in mouse ESCs. Structure-guided point mutants abrogated the Prdm14-Mtgr1 association and disrupted Prdm14's function in mESC gene expression and PGC formation in vitro. Altogether, our work uncovers the molecular mechanism underlying Prdm14-mediated repression. Examination of Prdm14 and Mtgr1 occupancy by ChIP-seq and effects on gene expression in mouse embryonic stem cells

2016-07-03 | E-GEOD-74547 | biostudies-arrayexpress

REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

Project description:Genome-wide analysis of REST and Polycomb binding in Rest-/- and Eed-/- mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG islands and the H3K27Me3 mark., and that PRC2 was frequently increased around Rest binding sites located in CpG-rich regions in the Rest2/2 mES cells. Published here: PLoS Genet 8(3): e1002494. doi:10.1371/journal.pgen.1002494 Examination of REST and Polycomb binding in Rest-/-, Eed-/-, and wt mES cells using ChIP-sequencing. Submitter cannot locate the raw data for GSM1169003, GSM1169004, GSM1169011, GSM1169012, GSM1169015, and GSM1169016.

2013-06-20 | E-GEOD-48122 | biostudies-arrayexpress

Variant PRC1 complex dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-05-27 | E-GEOD-55698 | biostudies-arrayexpress