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| 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.
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| 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.
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| Contributor(s) |
Dimitrova E, Klose RJ |
| Citation missing |
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| |
| Submission date |
Oct 14, 2021 |
| Last update date |
May 23, 2022 |
| Contact name |
Emilia Dimitrova |
| E-mail(s) |
[email protected]
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| Organization name |
University of Oxford
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| Department |
Biochemistry
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| Lab |
Rob Klose
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL25537 |
Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus) |
|
| Samples (32)
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| This SubSeries is part of SuperSeries: |
| GSE185930 |
Distinct roles of CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction |
|
| Relations |
| BioProject |
PRJNA771383 |
| SRA |
SRP341433 |
| 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 |
| GSE185929_Pcgf2fl_nucRNASeq_48hRA_TAM_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw |
78.4 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_48hRA_TAM_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw |
211.5 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_48hRA_UNT_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw |
77.6 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_48hRA_UNT_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw |
209.2 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_ESC_TAM_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw |
83.4 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_ESC_TAM_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw |
212.5 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_ESC_UNT_mm10_downsampledSpikeInInp_MERGED_FORWARD.bw |
78.0 Mb |
(ftp)(http) |
BW |
| GSE185929_Pcgf2fl_nucRNASeq_ESC_UNT_mm10_downsampledSpikeInInp_MERGED_MinusStrand.bw |
214.3 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_ESC_TAM_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw |
80.2 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_ESC_TAM_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw |
184.3 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_ESC_UNT_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw |
97.0 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_ESC_UNT_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw |
222.5 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_RA_TAM_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw |
72.9 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_RA_TAM_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw |
173.5 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_RA_UNT_mm10_downsampleddm6tomm10RNA_MERGED_FORWARD.bw |
72.0 Mb |
(ftp)(http) |
BW |
| GSE185929_nucRNAseq_MED13-13LcKO_RA_UNT_mm10_downsampleddm6tomm10RNA_MERGED_MinusStrand.bw |
176.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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