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Series GSE185929 Query DataSets for GSE185929
Status Public on May 23, 2022
Title Distinct roles for CDK-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction (RNA-Seq)
Organisms Drosophila melanogaster; Mus musculus
Experiment type Expression 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 Gene expression profiling using spike-in calibrated nuclear RNA-seq of embryonic stem cells in which CDK-MED (Med13/13l fl/fl) or cPRC1 can be conditionally removed upon addition of tamoxifen. Cells were induced with retinoic acid.
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 (1)
GPL25537 Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus)
Samples (32)
GSM5627435 Med1313lfl_ESC_UNT_rep1
GSM5627436 Med1313lfl_ESC_UNT_rep2
GSM5627437 Med1313lfl_ESC_UNT_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 PRJNA771383
SRA SRP341433

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Supplementary file Size Download File type/resource
GSE185929_Med13fl_RA.NucRNAseq_spikenormalised_DESeq2.csv.gz 4.0 Mb (ftp)(http) CSV
GSE185929_Med13fl_RA_UNT.vs.Med13fl_ESC_UNT.NucRNAseq_spikenormalised_DESeq2.csv.gz 3.7 Mb (ftp)(http) CSV
GSE185929_Pcgf2fl_RA.NucRNAseq_spikenormalised_DESeq2.csv.gz 3.8 Mb (ftp)(http) CSV
GSE185929_Pcgf2fl_RA_UNT.vs.Pcgf2fl_ESC_UNT.NucRNAseq_spikenormalised_DESeq2.csv.gz 3.6 Mb (ftp)(http) CSV 78.4 Mb (ftp)(http) BW 211.5 Mb (ftp)(http) BW 77.6 Mb (ftp)(http) BW 209.2 Mb (ftp)(http) BW 83.4 Mb (ftp)(http) BW 212.5 Mb (ftp)(http) BW 78.0 Mb (ftp)(http) BW 214.3 Mb (ftp)(http) BW 80.2 Mb (ftp)(http) BW 184.3 Mb (ftp)(http) BW 97.0 Mb (ftp)(http) BW 222.5 Mb (ftp)(http) BW 72.9 Mb (ftp)(http) BW 173.5 Mb (ftp)(http) BW 72.0 Mb (ftp)(http) BW 176.7 Mb (ftp)(http) BW
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