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Series GSE120201 Query DataSets for GSE120201
Status Public on Nov 30, 2018
Title Widespread backtracking by RNA pol II is a major effector of gene activation, 5’ pause release, termination and transcription elongation rate
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary In addition to phosphodiester bond formation, RNA polymerase II has an RNA endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and backtracked. We identified backtracking sites using mNET-seq in human cells expressing dominant-negative TFIIS (TFIISDN) that inhibits RNA cleavage and stabilizes backtracked complexes. Backtracking is most frequent within 2 kb of start sites, consistent with slow elongation early in transcription, and in 3’ flanking regions where termination is enhanced by TFIISDN. Inhibition of the rescue from backtracked pol II by TFIISDN impaired the escape from 5’ pause sites, the completion of long transcripts, and activation of stress-inducible genes. TFIISDN slowed elongation rates genome-wide by half as measured by sequencing nascent transcripts pulse labeled with Bromouridine (Bru-seq) and by anti-pol II ChIP-seq at time points after release of a DRB block. These results suggest that rescue of backtracked pol II by TFIIS is a major stimulus of elongation.
Overall design 66 samples
Contributor(s) Bentley D, Sheridan RM
Citation(s) 30503775
Submission date Sep 19, 2018
Last update date Aug 30, 2023
Contact name Ryan Sheridan
Organization name University of Colorado Anschutz Medical Campus
Street address 12801 East 17th Avenue
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (66)
GSM3395914 Bru_Dox_DMOG_r1
GSM3395915 Bru_Dox_DMOG_r2
GSM3395916 Bru_Dox_r1
BioProject PRJNA491943
SRA SRP162163

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Supplementary file Size Download File type/resource 7.7 Mb (ftp)(http) BW 7.5 Mb (ftp)(http) BW 10.1 Mb (ftp)(http) BW 9.8 Mb (ftp)(http) BW 10.9 Mb (ftp)(http) BW 10.5 Mb (ftp)(http) BW 11.9 Mb (ftp)(http) BW 11.5 Mb (ftp)(http) BW 45.9 Mb (ftp)(http) BW 44.6 Mb (ftp)(http) BW 36.4 Mb (ftp)(http) BW 35.3 Mb (ftp)(http) BW 19.7 Mb (ftp)(http) BW 19.1 Mb (ftp)(http) BW 43.8 Mb (ftp)(http) BW 42.5 Mb (ftp)(http) BW
GSE120201_RAW.tar 1.1 Gb (http)(custom) TAR (of BW) 62.3 Mb (ftp)(http) BW 48.3 Mb (ftp)(http) BW 17.7 Mb (ftp)(http) BW 77.2 Mb (ftp)(http) BW 70.6 Mb (ftp)(http) BW 18.7 Mb (ftp)(http) BW 34.7 Mb (ftp)(http) BW 13.9 Mb (ftp)(http) BW 33.2 Mb (ftp)(http) BW 28.9 Mb (ftp)(http) BW 34.8 Mb (ftp)(http) BW 28.5 Mb (ftp)(http) BW 30.1 Mb (ftp)(http) BW 31.6 Mb (ftp)(http) BW
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Processed data provided as supplementary file
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