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Series GSE126985 Query DataSets for GSE126985
Status Public on Jan 12, 2020
Title PRC1 facilitates stage-specific enhancer-promoter contacts during Drosophila development
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are highly conserved epigenetic factors that collaborate at multiple levels to maintain their target genes in a repressed state. However, recent reports suggest that PRC1 binds a subset of active promoters and enhancers devoid of the PRC2-mediated H3K27me3 repressive mark in both Drosophila and mammals. Here, we characterize the 3D epigenome of Drosophila Eye-antennal imaginal discs (EDs) and identify a large set of PRC1-bound promoters and enhancers that show preferential interactions in 3D. These PRC1-centered contacts are generally not pre-formed in embryos and coincide with increased PRC1 binding at the larval stage, a concomitant increase in expression during development and mis-regulation in PRC1 mutants. A detailed analysis of the dachshund locus indicates that PRC1-anchored chromatin loops are not only repressive structures, but might also be required for gene activation. Finally, a meta-analysis of RING1B binding profiles and 3D contacts during mouse neural differentiation suggests that this function might be conserved in mammals. These data suggest that, in addition to its known function in gene silencing, PRC1 binding to enhancers and promoters favors stage-specific 3D contacts to facilitate transcription of key developmental genes.
Overall design Characterization of the 3D epigenetic landscape of the Polycomb Repressive Complex 1 (PRC1) during Drosophila development using ChIP-Seq, RNA-Seq and Hi-C methods.

Please note that the *merge* processed files were generated by merging all the replicates and are linked to the corresponding rep1 sample records.
Contributor(s) Loubiere V, Papadopoulos GL, Szabo Q, Martinez AM, Cavalli G
Citation(s) 31950077
Submission date Feb 24, 2019
Last update date Jan 21, 2020
Contact name Vincent Loubiere
Phone +33663182164
Organization name UMR9002; CNRS-UM
Department Institute of Human Genetics
Lab Chromatin and Cellular Biology
Street address 141 rue de la Cardonille
City Montpellier
State/province FRANCE
ZIP/Postal code 34090
Country France
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (46)
GSM3619386 ChIP_H2AK118Ub_E1416_rep1
GSM3619387 ChIP_H2AK118Ub_E1416_rep2
GSM3619388 ChIP_H2AK118Ub_ED_rep1
BioProject PRJNA524004
SRA SRP186730

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
GSE126985_RAW.tar 16.4 Gb (http)(custom) TAR (of BED, BW, NARROWPEAK, TAR, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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