NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE159399 Query DataSets for GSE159399
Status Public on Jul 21, 2021
Title PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency [RNA-seq]
Organisms Drosophila melanogaster; Mus musculus
Experiment type Expression 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 gene expression using spike-in calibrated nuclear RNA-seq. Cells were treated with auxin for 2, 4, 8 or 24 hours in three independent biological replicates, and gene expression changes were analysed relative to the control untreated cells.
Another mouse ESC line in which PRC2 can be depleted via the dTAG-inducible degron system was profiled in a similar manner to compare gene expression before and after 2 hours treatment with dTAG-13 compound.
 
Contributor(s) Dobrinić P, Klose RJ
Citation(s) 34608337
Submission date Oct 12, 2020
Last update date Oct 20, 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 (1)
GPL25537 Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus)
Samples (21)
GSM4829013 RING1AKO.RING1BAID_NucRNA_UNT_rep1
GSM4829014 RING1AKO.RING1BAID_NucRNA_UNT_rep2
GSM4829015 RING1AKO.RING1BAID_NucRNA_UNT_rep3
This SubSeries is part of SuperSeries:
GSE159400 PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency
Relations
BioProject PRJNA668783
SRA SRP287149

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
GSE159399_RAW.tar 1.6 Gb (http)(custom) TAR (of BW)
GSE159399_RING1AKO.RING1BAID_spikenormalised_DESeq2_NucRNAseq_IAA_24h_vs_UNT.txt.gz 689.9 Kb (ftp)(http) TXT
GSE159399_RING1AKO.RING1BAID_spikenormalised_DESeq2_NucRNAseq_IAA_2h_vs_UNT.txt.gz 674.8 Kb (ftp)(http) TXT
GSE159399_RING1AKO.RING1BAID_spikenormalised_DESeq2_NucRNAseq_IAA_4h_vs_UNT.txt.gz 699.4 Kb (ftp)(http) TXT
GSE159399_RING1AKO.RING1BAID_spikenormalised_DESeq2_NucRNAseq_IAA_8h_vs_UNT.txt.gz 700.6 Kb (ftp)(http) TXT
GSE159399_SUZ12dTAG_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw 178.7 Mb (ftp)(http) BW
GSE159399_SUZ12dTAG_NucRNAseq_UNT_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw 165.6 Mb (ftp)(http) BW
GSE159399_SUZ12dTAG_NucRNAseq_dTAG_2h_mm10_mapped_sorted_rmdup_downsampled_MERGED_FORWARD.bw 184.5 Mb (ftp)(http) BW
GSE159399_SUZ12dTAG_NucRNAseq_dTAG_2h_mm10_mapped_sorted_rmdup_downsampled_MERGED_REVERSE.bw 168.5 Mb (ftp)(http) BW
GSE159399_SUZ12dTAG_spikenormalised_DESeq2_NucRNAseq_dTAG_2h_vs_UNT.txt.gz 586.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap