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Paused RNA polymerase II inhibits new transcriptional initiation


RNA polymerase II (Pol II) pauses downstream of the transcription initiation site before beginning productive elongation. This pause is a key component of metazoan gene expression regulation. Some promoters have a strong disposition for Pol II pausing and often mediate faster, more synchronous changes in expression. This requires multiple rounds of transcription and thus cannot rely solely on pause release. However, it is unclear how pausing affects the initiation of new transcripts during consecutive rounds of transcription. Using our recently developed ChIP-nexus method, we find that Pol II pausing inhibits new initiation. We propose that paused Pol II helps prevent new initiation between transcription bursts, which may reduce noise.

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Figure 1: ChIP-nexus detects the precise locations of basal transcription factors and Pol II along the core promoter in vivo.
Figure 2: Measurement of the half-lives of paused Pol II across the genome using triptolide treatment.
Figure 3: Promoters with stable Pol II pausing lack PICs but show downstream occupancy of TBP.
Figure 4: Paused Pol II inhibits new initiation.

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Gene Expression Omnibus

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We thank P. Verrijzer (Erasmus University Medical Center) for TAF2 antibodies, J. Kadonaga (University of California, San Diego) for TFIIA, TFIIB, TBP and TFIIF antibodies, J. Johnston for help with data analysis, and R. Krumlauf, R. Conaway, J. Conaway, C. Kaplan and R. Fropf for comments on the manuscript. The work was funded by the Stowers Institute for Medical Research.

Author information




W.S. and J.Z. conceived the project, W.S. performed all experiments and computational analyses, and W.S. and J.Z. interpreted the data and wrote the manuscript.

Corresponding author

Correspondence to Julia Zeitlinger.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 2–4 (PDF 9955 kb)

Supplementary Table 1

Summary of paused Pol II half-lives across the genome. (XLS 718 kb)

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Shao, W., Zeitlinger, J. Paused RNA polymerase II inhibits new transcriptional initiation. Nat Genet 49, 1045–1051 (2017).

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