Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

Charles G. Danko, Nasun Hah, Xin Luo, André L. Martins, Leighton Core, John T. Lis, Adam Siepel, W. Lee Kraus

Research output: Contribution to journalArticle

158 Citations (Scopus)

Abstract

RNA polymerase II (Pol II) transcribes hundreds of kilobases of DNA, limiting the production of mRNAs and lncRNAs. We used global run-on sequencing (GRO-seq) to measure the rates of transcription by Pol II following gene activation. Elongation rates vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pathways (i.e., 17β-estradiol [E2] and TNF-α). The rates are slowest near the promoter and increase during the first ∼15 kb transcribed. Gene body elongation rates correlate with Pol II density, resulting in systematically higher rates of transcript production at genes with higher Pol II density. Pol II dynamics following short inductions indicate that E2 stimulates gene expression by increasing Pol II initiation, whereas TNF-α reduces Pol II residence time at pause sites. Collectively, our results identify previously uncharacterized variation in the rate of transcription and highlight elongation as an important, variable, and regulated rate-limiting step during transcription.

Original languageEnglish (US)
Pages (from-to)212-222
Number of pages11
JournalMolecular Cell
Volume50
Issue number2
DOIs
StatePublished - Apr 25 2013

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RNA Polymerase II
Long Noncoding RNA
Transcriptional Activation
Genes
Estradiol
Gene Expression
Messenger RNA
DNA

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells. / Danko, Charles G.; Hah, Nasun; Luo, Xin; Martins, André L.; Core, Leighton; Lis, John T.; Siepel, Adam; Kraus, W. Lee.

In: Molecular Cell, Vol. 50, No. 2, 25.04.2013, p. 212-222.

Research output: Contribution to journalArticle

Danko, Charles G. ; Hah, Nasun ; Luo, Xin ; Martins, André L. ; Core, Leighton ; Lis, John T. ; Siepel, Adam ; Kraus, W. Lee. / Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells. In: Molecular Cell. 2013 ; Vol. 50, No. 2. pp. 212-222.
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