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Series GSE49078 Query DataSets for GSE49078
Status Public on Oct 31, 2013
Title Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals
Organism Drosophila melanogaster
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of short transcription start site-associated (tss) RNAs they produce. Here, we demonstrate that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 minutes at genes with inefficient pause release. Promoter-proximal termination by Pol II is infrequent and released tssRNAs are targeted for rapid degradation. Further, we provide evidence that the predominant tssRNA species observed are nascent RNAs held within early elongation complexes. We propose that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions.
 
Overall design This submission includes 13 raw data files. Four samples (chromatin, soluble, mock-treated, and Rrp40-depleted) are represented by two biological replicate raw data files, while five samples (cells, DMSO, FP, mock-treated + FP, and Rrp-40depleted + FP) are represented by single raw data files.
 
Contributor(s) Henriques T, Gilchrist DA, Nechaev S, Bern M, Muse G, Burkholder A, Fargo D, Adelman K
Citation(s) 24184211
Submission date Jul 22, 2013
Last update date May 15, 2019
Contact name Karen Adelman
E-mail(s) karen_adelman@hms.harvard.edu
Organization name Harvard Medical School
Department Biological Chemistry and Molecular Pharmacology
Street address 45 Shattuck St. LHRRB-201a
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL11203 Illumina Genome Analyzer IIx (Drosophila melanogaster)
Samples (9)
GSM1193420 Adelman_Dmel_S2_cells_3prRNA
GSM1193421 Adelman_Dmel_S2_chromatin_3prRNA
GSM1193422 Adelman_Dmel_S2_soluble_3prRNA
Relations
BioProject PRJNA212940
SRA SRP028120

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
GSE49078_RAW.tar 46.9 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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