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Series GSE42360 Query DataSets for GSE42360
Status Public on Apr 24, 2013
Title Genome-wide control of RNA polymerase II activity by cohesin (tiling)
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by genome tiling array
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 We performed ChIP-chip of Rpb3 (representing total Pol II), Ser2P-Pol II (representing elongating Pol II), and Cdk12 and CycT Pol II kinase components in Mock RNAi-treated and cohesin subunit Rad21 RNAi-treated ML-DmBG3-c2 cells, which revealed that cohesin depletion has a variety of effects on Pol II occupancy and modification, as well as on occupancy of Pol II kinases.
Contributor(s) Schaaf CA, Dorsett D
Citation(s) 23555293
Submission date Nov 16, 2012
Last update date Jul 08, 2015
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)
GPL6629 [DM_tiling2_MR] Affymetrix Drosophila Tiling 2.0R Array
Samples (8)
GSM1038323 Cdk12_BG3_Mock
GSM1038324 Cdk12_BG3_Rad21RNAi
GSM1038325 CycT_BG3_Mock
This SubSeries is part of SuperSeries:
GSE42399 Genome-wide control of RNA polymerase II activity by cohesin
BioProject PRJNA181292

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
GSE42360_Input_Repl1.CEL.gz 30.1 Mb (ftp)(http) CEL
GSE42360_Input_Repl2.CEL.gz 29.7 Mb (ftp)(http) CEL
GSE42360_Input_Repl3.CEL.gz 29.0 Mb (ftp)(http) CEL
GSE42360_RAW.tar 734.5 Mb (http)(custom) TAR (of BAR, BED, CEL)
Processed data provided as supplementary file

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