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Series GSE159398 Query DataSets for GSE159398
Status Public on Jul 21, 2021
Title PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [ChIP-seq]
Organisms Drosophila melanogaster; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The interrelatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population, and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.
Overall design Mouse embryonic stem cells in which PRC1 can be depleted via the auxin-inducible degron (AID) system were profiled for genomic distribution of Polycomb factors (RING1B, SUZ12), histone modifications (H2AK119ub1, H3K27me3, H3K4me3) and RNA polymerase II (total Pol II, Ser5P-Pol II, Ser2P-Pol II) using spike-in calibrated ChIP-seq. Cells were treated with auxin for 2, 4, 8 or 24 hours in three independent biological replicates.
Another mouse ESC line in which PRC2 can be depleted via the dTAG-inducible degron system was profiled in three independent biological replicates for genomic distribution of H3K27me3 before and after 2 hours treatment with dTAG-13 compound. Additionally, RING1B binding was compared between wild type (TIR1) and PRC1deg cells before auxin treatment, and H3K27me3 enrichment was compared between wild type (E14) and PRC2deg cell before dTAG-13 treatment.
Contributor(s) Dobrinić P, Klose RJ
Citation(s) 34608337
Submission date Oct 12, 2020
Last update date Oct 19, 2021
Contact name Paula Dobrinić
Organization name University of Oxford
Department Department of Biochemistry
Lab Rob Klose lab
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3QU
Country United Kingdom
Platforms (2)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
GPL25537 Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus)
Samples (154)
GSM4828883 RING1AKO.RING1BAID_H2AK119ub1_UNT_rep1
GSM4828884 RING1AKO.RING1BAID_H2AK119ub1_UNT_rep2
GSM4828885 RING1AKO.RING1BAID_H2AK119ub1_UNT_rep3
This SubSeries is part of SuperSeries:
GSE159400 PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency
BioProject PRJNA668782
SRA SRP287148

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

Supplementary file Size Download File type/resource 407.4 Mb (ftp)(http) BW
GSE159398_RAW.tar 10.0 Gb (http)(custom) TAR (of BW)
GSE159398_RING1B_peaks.bed.gz 64.6 Kb (ftp)(http) BED 168.5 Mb (ftp)(http) BW 185.4 Mb (ftp)(http) BW 500.5 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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