Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq for PRC2 components and H3K27me3 in E14 mouse embryonic stem cells

ABSTRACT: This experiment sought to determine the chromatin structure and PRC2 occupancy at the promoters of all genes in mouse ESCs ChIP-seq for EZH2, SUZ12, and H3K27me3 were performed on WT E14 cells in 2 biological replicates each. In addition H3K27me3 ChIP-seq was also performed on a clone of E14 cells expressing a tagged version of EZH2, which for the purpose of this study was used as replicate #3.

ORGANISM(S): Mus musculus

SUBMITTER: Roberto Bonasio

PROVIDER: E-GEOD-49431 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells.

Kaneko Syuzo S Son Jinsook J Shen Steven S SS Reinberg Danny D Bonasio Roberto R

Nature structural & molecular biology 20131020 11

EZH2 is the catalytic subunit of PRC2, a central epigenetic repressor essential for development processes in vivo and for the differentiation of embryonic stem cells (ESCs) in vitro. The biochemical function of PRC2 in depositing repressive H3K27me3 marks is well understood, but how it is regulated and directed to specific genes before and during differentiation remains unknown. Here, we report that PRC2 binds at low levels to a majority of promoters in mouse ESCs, including many that are active ...[more]

PMID: 24141703

Similar Datasets

CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [ChIP-Seq]

Project description:In this experiment, we sought to identify how the distribution of CTCF, H3K27me3, H3K4me3, Pol II, H2AK119Ub1, EZH2 3 lines (WT, Δ5|6, Δ5|6:7|9)

2015-02-26 | E-GEOD-60232 | biostudies-arrayexpress

ChIP-seq in MEG3+ and MEG3- hIPSCs

Project description:In this experiment we sought to identify region with differential PRC2, JARID2, and H3K27me3 occupancy in human induced pluripotent stem cell lines with silenced or expressed MEG3 locus to indirectly determine the effect of this ncRNA on PRC2 function. 8 hIPSC lines, 5 MEG3+ and 3 MEG3-; ChIP-seq for EZH2, JARID2, and H3K27me3. Some done in replicates.

2013-12-25 | E-GEOD-48516 | biostudies-arrayexpress

USP7 cooperates with SCML2 to regulate the activity of PRC1

Project description:In this experiment, we sought to identify the distribution of USP7 on chromatin relative to other PRC1 components ChIP-seq for USP7 in 293T-REx cells

2015-06-10 | E-GEOD-61048 | biostudies-arrayexpress

ChIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells

Project description:Polycomb repressive complex-1 (PRC1) is essential for the epigenetic regulation of gene expression. SCML2 is a mammalian homolog of Drosophila SCM, a Polycomb-group protein that associates with PRC1. Here, we show that SCML2A, an SCML2 isoform tightly associated to chromatin, contributes to PRC1 localization and also directly enforces repression of certain Polycomb target genes. SCML2A binds to PRC1 via its SPM domain and interacts with ncRNAs through a novel RNA-binding region (RBR). Targeting of SCML2A to chromatin involves the coordinated action of the MBT domains, RNA binding, and interaction with PRC1 through the SPM domain. Deletion of the RBR reduces the occupancy of SCML2A at target genes and overexpression of a mutant SCML2A lacking the RBR causes defects in PRC1 recruitment. These observations point to a role for ncRNAs in regulating SCML2 function and suggest that SCML2 participates in the epigenetic control of transcription directly and in cooperation with PRC1. This is the ChIP-seq part of the study

2014-07-02 | E-GEOD-38273 | biostudies-arrayexpress

ChIP-seq in MRC5 hIPSCs overexpressing MEG3 RNA.

Project description:This experiment was designed to detect differences in PRC2 occupancy in a human induced pluripotent cell line (MRC5) naturally deficient in MEG3 RNA after lentiviral overexpression of MEG3. MRC5 were transduced with lentiviruses for the overexpression of MEG3 lncRNA or GFP as a control. ChIP-seq was performed with EZH2 and JARID2 antibodies.

2013-12-25 | E-GEOD-48515 | biostudies-arrayexpress

RNA seq in two lines of E14 mouse embryonic stem cells

Project description:This experiment was designed to obtain the polyA+ transcriptome in E14 ESCs PolyA+ RNA was extracted and purified from two separate clones of E14, which were treated as biological replicate

2013-10-19 | E-GEOD-49434 | biostudies-arrayexpress

EZH2-RNA interactions in embryonic stem cells

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

2013-10-19 | E-GEOD-49435 | biostudies-arrayexpress

PAR-CLIP for HA-tagged EZH2 in mouse embryonic stem cells

Project description:This experiment was designed to indentify RNAs making direct contact with EZH2 in mouse embryonic stem cells E14 with an integrated transgene encoding HA-EZH2 were pulsed with 4-SU, irradiated with UV, and subjected to HA immunoprecipitation.

2013-10-19 | E-GEOD-49433 | biostudies-arrayexpress

Cell reprogramming requires silencing of a core subset of Polycomb targets.

Project description:Transcription factor (TF)-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is associated with genome-wide changes in chromatin modifications. Polycomb-mediated histone H3 lysine-27 trimethylation (H3K27me3) has been proposed as a defining mark that distinguishes the somatic from the iPSC epigenome. Here, we dissected the functional role of H3K27me3 in TF-induced reprogramming through the inactivation of the H3K27 methylase EZH2 at the onset of reprogramming. Our results demonstrate that surprisingly the establishment of functional iPSC proceeds despite global loss of H3K27me3. iPSC lacking EZH2 efficiently silenced the somatic transcriptome and differentiated into tissues derived from the three germ layers. Remarkably, the genome-wide analysis of H3K27me3 in Ezh2 mutant iPSC cells revealed the retention of this mark on a highly selected group of Polycomb targets enriched for developmental regulators controlling the expression of lineage specific genes. Erasure of H3K27me3 from these targets led to a striking impairment in TF-induced reprogramming. These results indicate that PRC2-mediated H3K27 trimethylation is required on a highly selective core of Polycomb targets whose repression enables TF-dependent cell reprogramming. Genechip microarray analysis was performed respectively on 4 Ezh2 +/+ iPSC clones (control), 4 Ezh2 M-bM-^HM-^FSET/M-bM-^HM-^FSET iPSC clones (experimental), 3 independent preparations of wild type MEF (reference) and one sample of E14Tg2a embryonic stem cells (reference) using Affymetrix Mouse Gene 1.0 ST arrays. Labeling, hybridization, and washing were performed according to Affymetrix guidelines

2013-03-09 | E-GEOD-44972 | biostudies-arrayexpress

Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin

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

2013-12-25 | E-GEOD-48518 | biostudies-arrayexpress