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Series GSE173860 Query DataSets for GSE173860
Status Public on Sep 29, 2021
Title The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Polycomb complexes have traditionally been prescribed roles as transcriptional repressors, though increasing evidence demonstrate they can also activate gene expression. However, the mechanisms underlying positive gene regulation mediated by Polycomb proteins are poorly understood. Here, we show that RING1B, a core component of Polycomb Repressive Complex 1, regulates enhancer-promoter interaction of the bona fide estrogen-activated GREB1 gene. Systematic characterization of RNA:DNA hybrid formation (R-loops), nascent transcription, and RNA Pol II activity upon estrogen administration revealed a key role of RING1B in gene activation by regulating R-loop formation and RNA Pol II elongation. We also found that the estrogen receptor (ER) and RNA are both necessary for full RING1B recruitment to estrogen-activated genes. Notably, RING1B recruitment was mostly unaffected upon RNA Pol II depletion by triptolide. Our findings delineate the functional interplay between RING1B, RNA, and ER to safeguard chromatin architecture perturbations required for estrogen-mediated gene regulation, and highlight the crosstalk between steroid hormones and Polycomb proteins to regulate oncogenic programs.
Overall design ChIP-seq of RING1B, ERa, and RNA Pol II in T47D cells treated with DMSO or Triptolide (10 uM) for 9 hours in HD and after 45' of E2 treatment. RING1B and ERa ChIP-seq are provided in duplicates. Pair-end ATAC-seq of T47D shCtrl and shRING1B cells in HD and after45' of E2 in duplicates. RNA-seq of T47D shCtrl and shRING1B cells in HD and after 45' of E2 in duplicates. RING1B and ERa rChIP of T47D cells treated with DMSO for 9 hours followed by E2 for 45' provided in duplicates. DRIP-seq of T47D cells in HD and after 45' of E2 along with negative controls. DRIP-seq of T47D shCtrl and shRING1B cells in HD and after 45' of E2 along with negative controls. 4C-seq of T47D shCtrl and shRING1B cells in HD and after 45' of E2.
Contributor(s) Zhang Y, Liu T, Yuan F, Garcia-Martinez L, Lee KD, Stransky S, Sidoli S, Verdun RE, Zhang Y, Wang Z, Morey L
Citation(s) 34428304
Submission date May 04, 2021
Last update date Sep 30, 2021
Contact name Lluis Morey
Organization name University of Miami Miller School of Medicine
Department Sylvester Comprehensive Cancer Center
Lab Morey Lab
Street address 1501 NW 10th Ave 742-H2
City Miami
State/province FL
ZIP/Postal code 33135
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (76)
GSM5281974 rep1_shCtrl_0hr_atacseq
GSM5281975 rep1_shRING1B_0hr_atacseq
GSM5281976 rep1_shCtrl_45min_atacseq
BioProject PRJNA727335
SRA SRP318473

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
GSE173860_01_DMSO_HD_RING1B_pooled.chip.fc.signal.bigwig 1.0 Gb (ftp)(http) BIGWIG
GSE173860_01_DMSO_HD_RING1B_rep1.chip.fc.signal.bigwig 789.2 Mb (ftp)(http) BIGWIG
GSE173860_01_DMSO_HD_RING1B_rep2.chip.fc.signal.bigwig 628.1 Mb (ftp)(http) BIGWIG
GSE173860_01_shCtrl_HD_pooled.atac.fc.signal.bigwig 1.4 Gb (ftp)(http) BIGWIG
GSE173860_02_DMSO_HD_ER_pooled.chip.fc.signal.bigwig 837.7 Mb (ftp)(http) BIGWIG
GSE173860_02_DMSO_HD_ER_rep1.chip.fc.signal.bigwig 458.7 Mb (ftp)(http) BIGWIG
GSE173860_02_DMSO_HD_ER_rep2.chip.fc.signal.bigwig 583.4 Mb (ftp)(http) BIGWIG
GSE173860_02_shRING1B_HD_pooled.atac.fc.signal.bigwig 81.7 Mb (ftp)(http) BIGWIG
GSE173860_03_DMSO_HD_RNAP_rep.chip.fc.signal.bigwig 563.8 Mb (ftp)(http) BIGWIG
GSE173860_03_shCtrl_E2_pooled.atac.fc.signal.bigwig 1.1 Gb (ftp)(http) BIGWIG
GSE173860_04_shRING1B_E2_pooled.atac.fc.signal.bigwig 229.9 Mb (ftp)(http) BIGWIG
GSE173860_05_Trip_HD_RING1B_pooled.chip.fc.signal.bigwig 1.0 Gb (ftp)(http) BIGWIG
GSE173860_05_Trip_HD_RING1B_rep1.chip.fc.signal.bigwig 684.1 Mb (ftp)(http) BIGWIG
GSE173860_05_Trip_HD_RING1B_rep2.chip.fc.signal.bigwig 684.8 Mb (ftp)(http) BIGWIG
GSE173860_06_Trip_HD_ER_pooled.chip.fc.signal.bigwig 934.2 Mb (ftp)(http) BIGWIG
GSE173860_06_Trip_HD_ER_rep1.chip.fc.signal.bigwig 507.2 Mb (ftp)(http) BIGWIG
GSE173860_06_Trip_HD_ER_rep2.chip.fc.signal.bigwig 682.3 Mb (ftp)(http) BIGWIG
GSE173860_07_Trip_HD_RNAP.chip.fc.signal.bigwig 538.1 Mb (ftp)(http) BIGWIG
GSE173860_09_DMSO_E2_RING1B_pooled.chip.fc.signal.bigwig 1.0 Gb (ftp)(http) BIGWIG
GSE173860_09_DMSO_E2_RING1B_rep1.chip.fc.signal.bigwig 677.9 Mb (ftp)(http) BIGWIG
GSE173860_09_DMSO_E2_RING1B_rep2.chip.fc.signal.bigwig 721.0 Mb (ftp)(http) BIGWIG
GSE173860_10_DMSO_E2_ER_pooled.chip.fc.signal.bigwig 954.9 Mb (ftp)(http) BIGWIG
GSE173860_10_DMSO_E2_ER_rep1.chip.fc.signal.bigwig 489.0 Mb (ftp)(http) BIGWIG
GSE173860_10_DMSO_E2_ER_rep2.chip.fc.signal.bigwig 721.6 Mb (ftp)(http) BIGWIG
GSE173860_11_DMSO_E2_RNAP.chip.fc.signal.bigwig 663.9 Mb (ftp)(http) BIGWIG
GSE173860_13_Trip_E2_RING1B_pooled.chip.fc.signal.bigwig 1.0 Gb (ftp)(http) BIGWIG
GSE173860_13_Trip_E2_RING1B_rep1.chip.fc.signal.bigwig 768.4 Mb (ftp)(http) BIGWIG
GSE173860_13_Trip_E2_RING1B_rep2.chip.fc.signal.bigwig 640.7 Mb (ftp)(http) BIGWIG
GSE173860_14_Trip_E2_ER_pooled.chip.fc.signal.bigwig 978.7 Mb (ftp)(http) BIGWIG
GSE173860_14_Trip_E2_ER_rep1.chip.fc.signal.bigwig 647.0 Mb (ftp)(http) BIGWIG
GSE173860_14_Trip_E2_ER_rep2.chip.fc.signal.bigwig 617.2 Mb (ftp)(http) BIGWIG
GSE173860_15_Trip_E2_RNAP.chip.fc.signal.bigwig 477.7 Mb (ftp)(http) BIGWIG
GSE173860_17_rChIP_ER_pooled.chip.fc.signal.bigwig 938.7 Mb (ftp)(http) BIGWIG
GSE173860_17_rChIP_ER_rep1.chip.fc.signal.bigwig 507.4 Mb (ftp)(http) BIGWIG
GSE173860_17_rChIP_ER_rep2.chip.fc.signal.bigwig 678.5 Mb (ftp)(http) BIGWIG
GSE173860_18_rChIP_RING1B_pooled.chip.fc.signal.bigwig 1.0 Gb (ftp)(http) BIGWIG
GSE173860_18_rChIP_RING1B_rep1.chip.fc.signal.bigwig 679.0 Mb (ftp)(http) BIGWIG
GSE173860_18_rChIP_RING1B_rep2.chip.fc.signal.bigwig 726.6 Mb (ftp)(http) BIGWIG
GSE173860_RAW.tar 885.1 Mb (http)(custom) TAR (of BIGWIG, BW, RESULTS, TXT)
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Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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