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Series GSE119618 Query DataSets for GSE119618
Status Public on Apr 26, 2019
Title Synergy between variant PRC1 complexes defines Polycomb-mediated gene repression (ChIP-Seq)
Organisms Drosophila melanogaster; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X-chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.
Overall design Mouse embryonic stem cells in which distinct PCGF-containing PRC1 complexes can be conditionally removed individually or in different combinations ( Pcgf4-/-; Pcgf2fl/fl, Pcgf1fl/fl, Pcgf3fl/fl, Pcgf5fl/fl, Pcgf6fl/fl, Pcgf3/5fl/fl, Pcgf1/3/5fl/fl, Pcgf1/3/5/2fl/fl, Pcgf1/3/5/6fl/fl and Ring1a-/-; Ring1bfl/fl) and Mus domesticus (129S1) x Mus castaneus F1 hybrid ESC line with inducible full-length Xist transgene were profiled for PRC1 (H2AK119ub1 and RING1B, as well as subunits specific for distinct PRC1 complexes - PCGF1, PCGF2, CBX7, and PHC1) and PRC2 (H3K27me3 and SUZ12) binding and activity using spike-in calibrated native (histone modifications) or cross-linked ChIP-seq (Polycomb factors).
Contributor(s) Fursova NA, Blackledge NP, Klose RJ
Citation(s) 31029541, 33563969
Submission date Sep 06, 2018
Last update date Mar 02, 2021
Contact name Nadezda A Fursova
Organization name University of Oxford
Department Department of Biochemistry
Lab Klose lab
Street address South Parks Rd
City Oxford
ZIP/Postal code OX13QU
Country United Kingdom
Platforms (2)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
GPL25537 Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus)
Samples (296)
GSM3379157 RING1Bfl_UNT_H2AK119ub1_rep1
GSM3379158 RING1Bfl_UNT_H2AK119ub1_rep2
GSM3379159 RING1Bfl_UNT_H2AK119ub1_rep3
This SubSeries is part of SuperSeries:
GSE119620 Synergy between variant PRC1 complexes defines Polycomb-mediated gene repression
BioProject PRJNA489754
SRA SRP160401

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Supplementary file Size Download File type/resource
GSE119618_ClassicalPolycombChromatinDomains.bed.gz 21.2 Kb (ftp)(http) BED
GSE119618_RING1B.peaks.bed.gz 79.2 Kb (ftp)(http) BED
GSE119618_SUZ12.peaks.bed.gz 54.9 Kb (ftp)(http) BED 279.0 Mb (ftp)(http) BW 225.8 Mb (ftp)(http) BW 229.2 Mb (ftp)(http) BW 174.3 Mb (ftp)(http) BW 90.5 Mb (ftp)(http) BW 68.2 Mb (ftp)(http) BW 90.2 Mb (ftp)(http) BW 68.2 Mb (ftp)(http) BW 383.3 Mb (ftp)(http) BW 503.9 Mb (ftp)(http) BW 166.2 Mb (ftp)(http) BW 464.1 Mb (ftp)(http) BW 523.0 Mb (ftp)(http) BW 166.7 Mb (ftp)(http) BW 165.8 Mb (ftp)(http) BW 560.6 Mb (ftp)(http) BW 193.8 Mb (ftp)(http) BW 522.7 Mb (ftp)(http) BW 573.0 Mb (ftp)(http) BW 194.0 Mb (ftp)(http) BW 345.7 Mb (ftp)(http) BW 488.4 Mb (ftp)(http) BW 157.8 Mb (ftp)(http) BW 487.9 Mb (ftp)(http) BW 560.3 Mb (ftp)(http) BW 157.6 Mb (ftp)(http) BW 66.0 Mb (ftp)(http) BW 397.1 Mb (ftp)(http) BW 207.2 Mb (ftp)(http) BW 503.6 Mb (ftp)(http) BW 488.3 Mb (ftp)(http) BW 207.1 Mb (ftp)(http) BW 70.4 Mb (ftp)(http) BW 244.9 Mb (ftp)(http) BW 617.6 Mb (ftp)(http) BW 609.3 Mb (ftp)(http) BW 178.6 Mb (ftp)(http) BW 178.4 Mb (ftp)(http) BW 141.0 Mb (ftp)(http) BW 352.2 Mb (ftp)(http) BW 442.4 Mb (ftp)(http) BW 616.1 Mb (ftp)(http) BW 141.2 Mb (ftp)(http) BW 416.9 Mb (ftp)(http) BW 484.2 Mb (ftp)(http) BW 647.4 Mb (ftp)(http) BW 72.7 Mb (ftp)(http) BW 72.5 Mb (ftp)(http) BW 544.8 Mb (ftp)(http) BW 492.1 Mb (ftp)(http) BW 193.2 Mb (ftp)(http) BW 526.3 Mb (ftp)(http) BW 396.1 Mb (ftp)(http) BW 192.6 Mb (ftp)(http) BW 391.0 Mb (ftp)(http) BW 469.2 Mb (ftp)(http) BW 207.0 Mb (ftp)(http) BW 157.0 Mb (ftp)(http) BW 611.2 Mb (ftp)(http) BW 504.7 Mb (ftp)(http) BW 390.5 Mb (ftp)(http) BW 406.1 Mb (ftp)(http) BW 207.3 Mb (ftp)(http) BW 157.0 Mb (ftp)(http) BW 648.4 Mb (ftp)(http) BW 502.8 Mb (ftp)(http) BW 256.3 Mb (ftp)(http) BW 559.2 Mb (ftp)(http) BW 175.2 Mb (ftp)(http) BW 626.3 Mb (ftp)(http) BW 595.4 Mb (ftp)(http) BW 175.1 Mb (ftp)(http) BW 183.1 Mb (ftp)(http) BW 186.0 Mb (ftp)(http) BW 69.8 Mb (ftp)(http) BW 69.4 Mb (ftp)(http) BW 537.0 Mb (ftp)(http) BW 195.7 Mb (ftp)(http) BW 565.6 Mb (ftp)(http) BW 132.6 Mb (ftp)(http) BW 495.4 Mb (ftp)(http) BW 249.1 Mb (ftp)(http) BW 568.6 Mb (ftp)(http) BW 133.0 Mb (ftp)(http) BW 514.7 Mb (ftp)(http) BW 173.8 Mb (ftp)(http) BW 477.7 Mb (ftp)(http) BW 173.6 Mb (ftp)(http) BW 501.4 Mb (ftp)(http) BW 165.9 Mb (ftp)(http) BW 536.2 Mb (ftp)(http) BW 166.0 Mb (ftp)(http) BW 534.4 Mb (ftp)(http) BW 147.3 Mb (ftp)(http) BW 294.2 Mb (ftp)(http) BW 41.1 Mb (ftp)(http) BW 101.9 Mb (ftp)(http) BW 490.3 Mb (ftp)(http) BW 147.2 Mb (ftp)(http) BW 514.2 Mb (ftp)(http) BW 651.1 Mb (ftp)(http) BW 99.6 Mb (ftp)(http) BW
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