1. Chromosomes and Gene Expression
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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
Research Article
  • Cited 34
  • Views 6,374
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Cite this article as: eLife 2017;6:e27451 doi: 10.7554/eLife.27451

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.

Reviewing Editor

  1. Antoine M van Oijen, University of Wollongong, Australia

Publication history

  1. Received: April 4, 2017
  2. Accepted: August 24, 2017
  3. Accepted Manuscript published: August 25, 2017 (version 1)
  4. Version of Record published: September 18, 2017 (version 2)
  5. Version of Record updated: February 12, 2018 (version 3)
  6. Version of Record updated: February 6, 2019 (version 4)

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.

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Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
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    The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. We developed a method to study these two processes at single base-pair resolution. Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein and by ChIP-seq to map the distribution of Sir3-M.EcoGII. A silencing-deficient mutant of Sir3 lacking its Bromo-Adjacent Homology (BAH) domain, sir3-bah∆, was still recruited to HML, HMR, and telomeres. However, in the absence of the BAH domain, it was unable to spread away from those recruitment sites. Overexpression of Sir3 did not lead to further spreading at HML, HMR, and most telomeres. A few exceptional telomeres, like 6R, exhibited a small amount of Sir3 spreading, suggesting that boundaries at telomeres responded variably to Sir3 overexpression. Finally, by using a temperature-sensitive allele of SIR3 fused to M.ECOGII, we tracked the positions first methylated after induction and found that repression of genes at HML and HMR began before Sir3 occupied the entire locus.