RNA Polymerase II cluster dynamics predict mRNA output in living cells

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.

Article and author information

Author details

  1. Won-Ki Cho

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Namrata Jayanth

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Brian P English

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Takuma Inoue

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. J Owen Andrews

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. William Conway

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Jonathan B Grimm

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Jan-Hendrik Spille

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Luke D Lavis

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Timothée Lionnet

    Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. 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

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

Publication history

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

Copyright

© 2016, Cho et al.

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.

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  1. Won-Ki Cho
  2. Namrata Jayanth
  3. Brian P English
  4. Takuma Inoue
  5. J Owen Andrews
  6. William Conway
  7. Jonathan B Grimm
  8. Jan-Hendrik Spille
  9. Luke D Lavis
  10. Timothée Lionnet
  11. Ibrahim I Cisse
(2016)
RNA Polymerase II cluster dynamics predict mRNA output in living cells
eLife 5:e13617.
https://doi.org/10.7554/eLife.13617
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