E-GEOD-42397 - Genome-wide control of RNA polymerase II activity by cohesin (sequencing)

Status
Released on 24 April 2013, last updated on 1 May 2013
Organism
Drosophila melanogaster
Samples (6)
Protocols (4)
Description
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. 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.
Experiment type
RNA-seq of coding RNA 
Contacts
Cheri A Schaaf <cheri.schaaf@gmail.com>, Amanda Koenig, Dale Dorsett, Hojoong Kwak, John T Lis, Ziva Misulovin
Citation
Genome-Wide Control of RNA Polymerase II Activity by Cohesin. Schaaf CA, Kwak H, Koenig A, Misulovin Z, Gohara DW, Watson A, Zhou Y, Lis JT, Dorsett D. , Europe PMC 23555293
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-42397.idf.txt
Sample and data relationshipE-GEOD-42397.sdrf.txt
Processed data (2)E-GEOD-42397.processed.1.zip, E-GEOD-42397.processed.2.zip
Links