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.

Reviewing Editor

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

Version 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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  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

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

Further reading

    1. Chromosomes and Gene Expression
    Rachel A Johnston, Katherine A Aracena ... Jenny Tung
    Research Advance

    Previously, we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here, we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures—one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.