RNA Polymerase II cluster dynamics predict mRNA output in living cells

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Cite this article as: eLife 2016;5:e13617 doi: 10.7554/eLife.13617

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Abstract

Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output.

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Won-Ki Cho

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Namrata Jayanth

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Brian P English

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Takuma Inoue

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
J Owen Andrews

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
William Conway

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Jonathan B Grimm

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Jan-Hendrik Spille

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Luke D Lavis

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Timothée Lionnet

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

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The authors declare that no competing interests exist.
Ibrahim I Cisse

Department of Physics, Massachusetts Institute of Technology, Cambridge, United States

For correspondence
icisse@mit.edu

Competing interests
The authors declare that no competing interests exist.

Reviewing Editor

Xiaowei Zhuang, Howard Hughes Medical Institute, Harvard University, United States

Publication history

Received: December 8, 2015
Accepted: May 2, 2016
Accepted Manuscript published: May 3, 2016 (version 1)
Version of Record published: June 30, 2016 (version 2)

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.