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Series GSE42397 Query DataSets for GSE42397
Status Public on Apr 24, 2013
Title Genome-wide control of RNA polymerase II activity by cohesin (sequencing)
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin’s roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. On average, cohesin-binding genes have more transcriptionally active Pol II and promoter-proximal Pol II pausing than non-binding genes, and are more efficient, producing higher steady state levels of mRNA per transcribing Pol II complex. Cohesin depletion frequently increases pausing at cohesin-binding genes, indicating that cohesin often facilitates transition of paused Pol II to elongation. In many cases this likely reflects a role for cohesin in transcriptional enhancer function. Strikingly, more than 95% of predicted extragenic enhancers bind cohesin, and cohesin depletion can reduce their association with Pol II, indicating that cohesin facilitates enhancer-promoter contact. Cohesin directly promotes transcription of the myc gene, and cohesin depletion reduces Pol II activity at most Myc target genes. The multiple transcriptional roles of cohesin revealed by these studies likely underlie the growth and developmental deficits caused by minor changes in cohesin activity.
Overall design The PRO-seq method was used to measure transcriptionally engaged Pol II genome-wide in two replicates each of mock RNAi-treated, Nipped-B RNAi-treated, and Rad21 RNAi-treated ML-DmBG3-c2 cells.
Contributor(s) Schaaf CA, Kwak H, Misulovin Z, Koenig A, Lis JT, Dorsett D
Citation(s) 23555293
Submission date Nov 19, 2012
Last update date May 15, 2019
Contact name Cheri A Schaaf
Phone 314-977-9224
Organization name Saint Louis University School of Medicine
Department Biochemistry & Molecular Biology
Lab Dorsett
Street address 1100 South Grand Ave
City St Louis
State/province MO
ZIP/Postal code 63104
Country USA
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (6)
GSM1039189 BG3_Mock_PROseq_Rep1
GSM1039190 BG3_Mock_PROseq_Rep2
GSM1039191 BG3_Rad21RNAi_PROseq_Rep1
This SubSeries is part of SuperSeries:
GSE42399 Genome-wide control of RNA polymerase II activity by cohesin
BioProject PRJNA181291
SRA SRP017251

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Supplementary file Size Download File type/resource
GSE42397_RAW.tar 149.0 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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