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Series GSE41324 Query DataSets for GSE41324
Status Public on Apr 10, 2013
Title Signaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: Estrogen dependent signaling in MCF-7 cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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.
Overall design Using GRO-seq over a time course (0, 10, 25, and 40 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.
Contributor(s) Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL
Citation(s) 23523369
Submission date Oct 03, 2012
Last update date May 15, 2019
Contact name W. Lee Kraus
Organization name UT Southwestern Medical Center
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-8511
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (11)
GSM1014637 GRO-seq_Vehicle_MCF7_1
GSM1014638 GRO-seq_Vehicle_MCF7_2
GSM1014639 GRO-seq_Vehicle_MCF7_3
BioProject PRJNA176560
SRA SRP015988

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Supplementary file Size Download File type/resource
GSE41324_MCF7.10-40m.regressionRate.tsv.gz 2.6 Kb (ftp)(http) TSV
GSE41324_MCF7.25m.regressionRate.tsv.gz 1.6 Kb (ftp)(http) TSV
GSE41324_MCF7.40m.regressionRate.tsv.gz 3.1 Kb (ftp)(http) TSV
GSE41324_RAW.tar 462.9 Mb (http)(custom) TAR (of BED)
GSE41324_readme.txt 478 b (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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