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Series GSE138354 Query DataSets for GSE138354
Status Public on Feb 03, 2021
Title Enhancers predominantly control transcription initiation [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Gene transcription occurs via a cycle of linked events including initiation, promoter proximal pausing and elongation of RNA polymerase II (Pol 2). A key question is how do transcriptional enhancers influence these events to control gene expression? Here we have used a new approach to quantify transcriptional initiation and pausing in-vivo, while simultaneously identifying transcription start sites (TSSs) and pause-sites (TPSs). When analysed in parallel with nascent RNA-seq, these data show that differential gene expression is achieved predominantly via changes in transcription initiation rather than Pol 2 pausing or elongation. Using genetically engineered mouse models deleted for specific enhancers we show that these elements control gene expression via Pol 2 recruitment and/or initiation rather than via promoter proximal pause release. Using genome-wide analysis we show that enhancers, in general, control gene expression at the stage of Pol 2 recruitment and initiation rather than via pausing.
 
Overall design To characterise Pol2 density genome wide we performed ChIP-seq on primary mouse erythroid cells. A 10% input sample was taken from a wildtype sample prior to immunoprecipitation as a control and 5ng of this material was subjected to library prep alongside the immunoprecipitated samples.

HS2HS3 genotype: HS2 and HS3 enhancers of beta globin are homozygously deleted in combination
R1R2 genotype: A compound homozygous deletion of the R1 and R2 (a.k.a -26 and -31) transcriptional enhancers of the alpha globin gene (first reported in Hay et al 2016, Nature Genetics).
 
Contributor(s) Larke M, Sharpe JA, Sloane-Stanley JA, Butler S, Hughes JR, Higgs DR
Citation(s) 33539786
Submission date Oct 02, 2019
Last update date Jan 20, 2022
Contact name Martin Stephen Charles Larke
E-mail(s) martinlarke@gmail.com
Organization name University of Oxford
Department MRC Weatherall Institute of Molecular Medicine
Lab Hughes
Street address Headley Way
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM4105949 ChIP-seq Pol2 Mouse Wildtype fetal liver cells replicate 1
GSM4105950 ChIP-seq Pol2 Mouse Wildtype fetal liver cells replicate 2
GSM4105951 ChIP-seq Pol2 Mouse Wildtype fetal liver cells replicate 3
This SubSeries is part of SuperSeries:
GSE138359 Enhancers predominantly control transcription initiation
Relations
BioProject PRJNA575560

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
GSE138354_ahom.rpmpeaks.bw 905.9 Mb (ftp)(http) BW
GSE138354_bhom.rpmpeaks.bw 414.1 Mb (ftp)(http) BW
GSE138354_input_24h.bw 202.1 Mb (ftp)(http) BW
GSE138354_wt_vs_ahom.rpmpeaks.bw 1.1 Gb (ftp)(http) BW
GSE138354_wt_vs_bhom.rpmpeaks.bw 775.8 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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