Transcription factor clusters regulate genes in eukaryotic cells

  1. Adam JM Wollman
  2. Sviatlana Shashkova
  3. Erik G Hedlund
  4. Rosmarie Friemann
  5. Stefan Hohmann
  6. Mark C Leake  Is a corresponding author
  1. University of York, United Kingdom
  2. University of Gothenburg, Sweden

Abstract

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae. We find the repressor operates in clusters, which upon extracellular signal detection, translocate from the cytoplasm, bind to nuclear targets and turnover. Simulations of Mig1 configuration within a 3D yeast genome model combined with a promoter-specific, fluorescent translation reporter confirmed clusters are the functional unit of gene regulation. In vitro and structural analysis on reconstituted Mig1 suggests that clusters are stabilized by depletion forces between intrinsically disordered sequences. We observed similar clusters of a co-regulatory activator from a different pathway,  supporting a generalized cluster model for transcription factors that reduces promoter search times through intersegment transfer while stabilizing gene expression.

Article and author information

Author details

  1. Adam JM Wollman

    Biological Physical Sciences Institute, University of York, York, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Sviatlana Shashkova

    Biological Physical Sciences Institute, University of York, York, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4641-3295
  3. Erik G Hedlund

    Biological Physical Sciences Institute, University of York, York, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Rosmarie Friemann

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  5. Stefan Hohmann

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  6. Mark C Leake

    Biological Physical Sciences Institute, University of York, York, United Kingdom
    For correspondence
    mark.leake@york.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1715-1249

Funding

Biotechnology and Biological Sciences Research Council (grant BB/N006453/1)

  • Adam JM Wollman
  • Mark C Leake

Medical Research Council (MR/K01580X/1)

  • Mark C Leake

European Commission (289995)

  • Sviatlana Shashkova
  • Erik G Hedlund

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2017, Wollman 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.

Metrics

  • 7,594
    views
  • 1,133
    downloads
  • 86
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Adam JM Wollman
  2. Sviatlana Shashkova
  3. Erik G Hedlund
  4. Rosmarie Friemann
  5. Stefan Hohmann
  6. Mark C Leake
(2017)
Transcription factor clusters regulate genes in eukaryotic cells
eLife 6:e27451.
https://doi.org/10.7554/eLife.27451

Share this article

https://doi.org/10.7554/eLife.27451

Further reading

    1. Chromosomes and Gene Expression
    Shihui Chen, Carolyn Marie Phillips
    Research Article

    RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.