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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2013 |
| Title |
Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: TNF-alpha dependent signaling in AC16 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation. We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pathways (i.e., estrogen and TNFα). Elongation rates are slowest near the promoter and increase during the first ~15 kb transcribed into the gene body. Gene body elongation rates correlate with the density of Pol II, consequently resulting in systematically higher rates of transcript production at genes with higher Pol II density. By monitoring Pol II dynamics following short inductions, we found that E2 stimulates gene expression by increasing Pol II initiation, whereas TNFα stimulates the release of Pol II from promoter proximal pause sites. Collectively, our results identify previously uncharacterized variation in the rate of Pol II elongation and highlight elongation as an important, variable, and regulated rate limiting step in the transcription cycle.
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| Overall design |
Using GRO-seq over a time course (0, 10, and 30 min) of
TNFa signaling in AC16, immortalized adult human ventricular cardiomyocyte cells.
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| Contributor(s) |
Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL |
| Citation(s) |
23523369 |
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| Submission date |
Oct 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
[email protected]
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| Organization name |
UT Southwestern Medical Center
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| Street address |
5323 Harry Hines Blvd.
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA176559 |
| SRA |
SRP015987 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41323_AC16.regressionRate.tsv.gz |
833 b |
(ftp)(http) |
TSV |
| GSE41323_RAW.tar |
749.6 Mb |
(http)(custom) |
TAR (of BED) |
| GSE41323_readme.txt |
478 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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