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Series GSE138353 Query DataSets for GSE138353
Status Public on Feb 03, 2021
Title Enhancers predominantly control transcription initiation [Capture-C]
Organism Mus musculus
Experiment type Other
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 NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments; in this case haemoglobin alpha (hba-a1) haemoglobin beta (Hbb-b1) and mitoferrin (slc25a37), were used as viewpoints. The method was applied to primary mouse fetal liver erythroid cells in which the HS2 and HS3 enhancers of beta globin are homozygously deleted in combination. Wildtype and R1R2 KO have been published and data were deposited under GSE78803.
 
Contributor(s) Larke M, Downes DJ, Marieke Oudelaar A, 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 (3)
GSM4105946 NG-Capture-C Mouse HS2HS3 fetal liver cells replicate 1
GSM4105947 NG-Capture-C Mouse HS2HS3 fetal liver cells replicate 2
GSM4105948 NG-Capture-C Mouse HS2HS3 fetal liver cells replicate 3
This SubSeries is part of SuperSeries:
GSE138359 Enhancers predominantly control transcription initiation
Relations
BioProject PRJNA575561

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Supplementary file Size Download File type/resource
GSE138353_Beta_Enh_HS2HS3_HbbCombined_cis.gfc.txt.gz 400.8 Kb (ftp)(http) TXT
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Processed data are available on Series record

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