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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
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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.
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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).
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Contributor(s) |
Larke M, Sharpe JA, Sloane-Stanley JA, Butler S, Hughes JR, Higgs DR |
Citation(s) |
33539786 |
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Submission date |
Oct 02, 2019 |
Last update date |
Jan 20, 2022 |
Contact name |
Martin Stephen Charles Larke |
E-mail(s) |
martinlarke@gmail.com
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Organization name |
University of Oxford
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Department |
MRC Weatherall Institute of Molecular Medicine
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Lab |
Hughes
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Street address |
Headley Way
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City |
Oxford |
State/province |
Oxfordshire |
ZIP/Postal code |
OX3 9DS |
Country |
United Kingdom |
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Platforms (1) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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Samples (10)
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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 |
GSM4105952 |
ChIP-seq Pol2 Mouse R1R2 fetal liver cells replicate 1 |
GSM4105953 |
ChIP-seq Pol2 Mouse R1R2 fetal liver cells replicate 2 |
GSM4105954 |
ChIP-seq Pol2 Mouse R1R2 fetal liver cells replicate 3 |
GSM4105955 |
ChIP-seq Pol2 Mouse HS2HS3 fetal liver cells replicate 1 |
GSM4105956 |
ChIP-seq Pol2 Mouse HS2HS3 fetal liver cells replicate 2 |
GSM4105957 |
ChIP-seq Pol2 Mouse HS2HS3 fetal liver cells replicate 3 |
GSM4105958 |
ChIP-seq Input Mouse Wildtype fetal liver |
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This SubSeries is part of SuperSeries: |
GSE138359 |
Enhancers predominantly control transcription initiation |
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Relations |
BioProject |
PRJNA575560 |