GEO DataSets

(Submitter supplied) Polycomb repressive complex 2 (PRC2), a key regulator of metazoan development, induces transcriptional silencing by organizing repressive chromatin structures. To understand PRC2 associated genome topology, we performed chromatin interaction analyses focusing on three core subunits of PRC2 in embryonic stem cells (ESCs). Our comprehensive and high-resolution PRC2 interactome reveals connectivity networks manifested by the extensive looping between distal regulatory elements (DREs) and genes controlling differentiation. more...

Organism:

Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

5 related Platforms

107 Samples

Download data: BIGWIG, BROADPEAK, FPKM_TRACKING, HIC, NARROWPEAK, TXT

(Submitter supplied) STARR-seq assay performed on uncharacterized cis-regulatory elements to find candidate silencer elements in K562 cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL17275 GPL21306

34 Samples

Download data: TXT, XLS

(Submitter supplied) We generated HiC data from sorted mesodermal and non-mesodermal cells from stage 11-12 Drosophila embryos to explore the distribution of genomic contacts of silencers and non-silencers (identified elsewhere in the manuscript).

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL21306

4 Samples

Download data: TXT

(Submitter supplied) Silencers active in the Drosophila embryonic mesoderm were identified by reporter assays in dissociated embryonic cells. We find that, despite the presence of ChIP peaks for known transcriptional corepressors and marks of repressed chromatin, the only significantly enriched source of mesodermal silencers is non-mesodermal enhancers. We present evidence that a subset of silencers acts by looping to target promoters.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL17275

30 Samples

Download data: TXT, XLS

(Submitter supplied) Pluripotent embryonic stem (ES) cells constitute an essential cellular niche in animal development. It is well documented that ES cells are sustained by epigenetic and transcriptional regulation, but the role of post-transcriptional processes remains less explored. Here, we identify a link between nuclear RNA levels, regulated by the ‘polyA RNA exosome targeting’ (PAXT) connection, and transcriptional control, regulated by the Polycomb Repressive Complex 2 (PRC2). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL23479 GPL21626

41 Samples

Download data: BW

(Submitter supplied) The majority of the human genome does not encode proteins. Many of these noncoding regions contain important regulatory sequences that control gene expression. To date, most studies have focused on activators such as enhancers, but regions that repress gene expression⎯silencers⎯have not been systematically studied. We have developed a system that identifies silencer regions in a genome-wide fashion based on silencer-mediated transcriptional repression of caspase 9. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL20301 GPL15520

12 Samples

Download data: BED

(Submitter supplied) Preventing inappropriate gene expression in time and space is as fundamental as triggering the activation of tissue/cell-type specific factors at the correct developmental stage and in the correct cells. Here, we study the impact of Polycomb Repressive Complex 2 (PRC2) function on HoxA gene regulation. We analyze chromatin conformation of the HoxA cluster and its regulatory regions and show that in addition to the well-known role of PRC2 in silencing Hox genes via direct binding, its function is required for the changes in HoxA long-range interactions distinguishing proximal limb from distal limb. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

21 Samples

Download data: BIGWIG

(Submitter supplied) Polycomb repressive complex 2 and the epigenetic mark that it deposits, H3K27me3, are evolutionarily conserved and play critical roles in development and cancer. However, their roles in cell fate decisions in early embryonic development remain poorly understood. Here we report that knockout of polycomb repressive complex 2 genes in human embryonic stem cells causes pluripotency loss and spontaneous differentiation toward a meso-endoderm fate, owing to de-repression of BMP signalling. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

19 Samples

Download data: TXT

(Submitter supplied) Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of the global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21103 GPL25431 GPL19057

37 Samples

Download data: BW, TXT

(Submitter supplied) Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which characterizes many silenced genes including those on the inactive X-chromosome. Here we interrogate the role of core PRC2 protein EED in X-linked gene silencing by assessing allele-specific X-linked gene expression in WT and Eed-/- hybrid mouse trophoblast stem cells (TSCs) harboring a 129/S1-derived maternal X-chromosome and a JF1/Ms-derived paternal X-chromosome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

7 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) This experiment was designed to indentify RNAs making direct contact JARID2 as mouse ESCs differentiate

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: BED

(Submitter supplied) We report that Jarid2 is methylated at K116 by the polycomb complex PRC2. We analyzed Jarid2 versus Methylated Jarid2 genomic localization by ChIP-seq. We also study H3K27 enrichment in Jarid2 knock out ES cells and in cells rescued for Jarid2 or a mutant that cannot be methylated. ChIP-seq for H3K27me3 was perfomed in undiffrentiated ES cells as well as after 8 days of diffrentiation toward Embroyid Bodies (Hanging Drop method).

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

16 Samples

Download data: BIGWIG, BROADPEAK, TXT

(Submitter supplied) Increasing evidence suggests that diverse RNA binding proteins interact with regulatory RNAs to regulate transcription. RBFox2 is a ubiquitous RNA binding protein with prevalent expression in stem cells, heart, and brain. Here, we report a systematic dissection of the RBFox2-regulated RNA program in the mouse heart, demonstrating its essential function for organizing the contractile apparatus and excitation-contraction (EC) coupling by modulating alternative splicing and microRNA activity. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL13112

33 Samples

Download data: BW, XLSX

(Submitter supplied) VAL1 and 2 recruit SWN to targets

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: BW, XLS

(Submitter supplied) The Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) to repress gene transcription in multicellular eukaryotes. Despite its importance in gene silencing and cellular differentiation, how PRC2 is recruited to target loci is still not fully understood. Here, we report genome-wide evidence for the recruitment of PRC2 by the transcriptional repressors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 in Arabidopsis thaliana. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: TXT

(Submitter supplied) 14-day-old seedling of WT, val1, val2, and val1val2 were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21785

12 Samples

Download data: TXT

(Submitter supplied) Short tandem repeats are important contributors to silencer elements in T cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BW

(Submitter supplied) The Polycomb repressive complexes PRC1 and PRC2 act non-redundantly at target genes to maintain transcriptional programs and ensure cellular identity. PRC2 methylates lysine 27 on histone H3 (H3K27me), while PRC1 mono-ubiquitinates histone H2A at lysine 119 (H2Aub1). Here we present engineered mouse embryonic stem cells (ESCs) targeting the PRC2 subunits EZH1 and EZH2 to discriminate between contributions of distinct H3K27 methylation states and the presence of PRC2/1 at chromatin. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL13112

50 Samples

Download data: GAPPEDPEAK, NARROWPEAK, TXT

(Submitter supplied) The transcriptional repressors Polycomb Repressive Complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyse distinct histone modifications, establishing repressive chromatin at shared targets. Loss of PRC1, but not PRC2, from mouse embryonic stem cells (mESCs) triggers exit from pluripotency. How PRC2 and PRC1, which consists of distinct “variant PRC1” (vPRC1) and “canonical PRC1” (cPRC1) complexes, cooperate to silence genes and support mESC self-renewal is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

198 Samples

Download data: BW, TSV