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Series GSE185927 Query DataSets for GSE185927
Status Public on May 23, 2022
Title Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction (ChIP-Seq)
Organisms Drosophila melanogaster; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Precise control of gene expression is essential for normal development. This is thought to rely on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs) the CDK-Mediator (CDK-MED) complex has been reported to topologically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here we discover that CDK-MED contributes little to overall genome organisation in ESCs, but interestingly has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by the Polycomb repressive complexes (PRCs). These interactions are facilitated by CDK-MED but rely on canonical PRC1. However, through separation of function experiments, we reveal that the collaboration between CDK-MED and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on a topology-independent mechanism whereby the CDK module supports core Mediator engagement with gene promoters to support gene activation.
Overall design Genomic distribution of Polycomb (canonical PRC1 and H3K27me3), CDK-Mediator (CDK8) and core Mediator (MED14) was profiled in Med13/13l fl/fl ESCs, in which the CDK-Mediator can be conditionally disrupted. Genomic distribution of CDK-Mediator (CDK8) was profiled in Pcgf4-/-Pcgf2 fl/fl ESCs, in which the canonical PRC1 can be conditionally depleted.
Contributor(s) Dimitrova E, Klose RJ
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Submission date Oct 14, 2021
Last update date May 23, 2022
Contact name Emilia Dimitrova
Organization name University of Oxford
Department Biochemistry
Lab Rob Klose
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3QU
Country United Kingdom
Platforms (3)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
GPL25537 Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus)
Samples (81)
GSM5627352 Med1313lfl_UNT_CDK8_rep1
GSM5627353 Med1313lfl_UNT_CDK8_rep2
GSM5627354 Med1313lfl_UNT_CDK8_rep3
This SubSeries is part of SuperSeries:
GSE185930 Distinct roles of CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction
BioProject PRJNA771384
SRA SRP341432

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Supplementary file Size Download File type/resource 671.9 Mb (ftp)(http) BW 772.1 Mb (ftp)(http) BW 447.9 Mb (ftp)(http) BW 501.9 Mb (ftp)(http) BW 439.6 Mb (ftp)(http) BW 470.0 Mb (ftp)(http) BW 734.8 Mb (ftp)(http) BW 637.9 Mb (ftp)(http) BW 411.6 Mb (ftp)(http) BW 411.1 Mb (ftp)(http) BW 411.4 Mb (ftp)(http) BW 469.7 Mb (ftp)(http) BW 412.6 Mb (ftp)(http) BW 701.5 Mb (ftp)(http) BW 737.7 Mb (ftp)(http) BW 634.3 Mb (ftp)(http) BW 636.7 Mb (ftp)(http) BW
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