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Series GSE120393 Query DataSets for GSE120393
Status Public on Jan 07, 2020
Title Polycomb Mediated Chromatin Organization Reveals Transcriptional Silencers Required for Embryonic Development
Organism Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary 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. The deletion of these non-coding DREs in mice results in transcriptional de-repression and embryonic lethality. While functioning as silencers in ESCs, these DREs can transition into active enhancers during development, suggesting their dual regulatory activities. Integrative analysis of the three dimensional genome organization and spatial clusters of PRC2-chromatin hubs reveals the compact, peripheral assembly as the structural basis of the silencing compartments. Our study uncovers the molecular identity of PRC2 silencers, their associated genome architectures, and offers the exciting possibility of targeted re-activation of epigenetically silenced genes.
Overall design 1. Chromatin interaction analyses focusing on three core subunits of PRC2 (Eed, Ezh2, Suz12) in embryonic stem cells (ESCs) were performed to understand PRC2 associated genome topology and identify the distal regulatory elements (DREs).
2. Regulation activities of the DREs studied with the deletion of non-coding DREs in mice.
Contributor(s) Wei C, Ngan CY, Tjong H, Wong C
Citation(s) 32094912
Submission date Sep 24, 2018
Last update date Mar 04, 2020
Contact name Chia-Lin Wei
Phone 8608372049
Organization name The Jackson Laboratory
Department Genome Technologies
Street address 10 Discovery Drive
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
Platforms (5)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (107)
GSM3399651 SUZ12_chiapet_rep1
GSM3399652 SUZ12_chiapet_rep2
GSM3399653 SUZ12_chiapet_rep3
BioProject PRJNA492929
SRA SRP162484

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120393_ATAC-seq.bigWig 389.2 Mb (ftp)(http) BIGWIG
GSE120393_B6NJ_Ezh2chiapet.merged.hic 306.6 Mb (ftp)(http) HIC
GSE120393_CTCF_ChIP.narrowPeak.gz 918.7 Kb (ftp)(http) NARROWPEAK
GSE120393_CTCF_ChIP_foldEnrich.bigWig 720.5 Mb (ftp)(http) BIGWIG
GSE120393_CTCF_ChIP_input.bigWig 210.0 Mb (ftp)(http) BIGWIG
GSE120393_CTCF_ChIP_treat.bigWig 427.0 Mb (ftp)(http) BIGWIG
GSE120393_H3K27me3_ChIP.broadPeak.gz 106.2 Kb (ftp)(http) BROADPEAK
GSE120393_H3K27me3_ChIP_foldEnrich.bigWig 396.5 Mb (ftp)(http) BIGWIG
GSE120393_H3K27me3_ChIP_input.bigWig 161.0 Mb (ftp)(http) BIGWIG
GSE120393_H3K27me3_ChIP_treat.bigWig 213.2 Mb (ftp)(http) BIGWIG
GSE120393_KO18_Ezh2chiapet.merged.hic 607.7 Mb (ftp)(http) HIC
GSE120393_KO6_Ezh2chiapet.merged.hic 595.2 Mb (ftp)(http) HIC
GSE120393_RAW.tar 10.2 Mb (http)(custom) TAR (of FPKM_TRACKING, TXT)
GSE120393_RNAPolII_ChIP.narrowPeak.gz 513.6 Kb (ftp)(http) NARROWPEAK
GSE120393_RNAPolII_ChIP_foldEnrich.bigWig 593.4 Mb (ftp)(http) BIGWIG
GSE120393_RNAPolII_ChIP_input.bigWig 229.6 Mb (ftp)(http) BIGWIG
GSE120393_RNAPolII_ChIP_treat.bigWig 301.9 Mb (ftp)(http) BIGWIG
GSE120393_RNAPolII_chiapet.narrowPeak.gz 1.8 Mb (ftp)(http) NARROWPEAK
GSE120393_allPRC2.cis.chiasig.sigf.interactions.txt.gz 8.0 Mb (ftp)(http) TXT
GSE120393_allPRC2_chiapet.narrowPeak.gz 636.0 Kb (ftp)(http) NARROWPEAK
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