Nuclear microenvironments modulate transcription from low-affinity enhancers

  1. Albert Tsai  Is a corresponding author
  2. Anand K Muthusamy
  3. Mariana RP Alves
  4. Luke D Lavis
  5. Robert H Singer
  6. David L Stern
  7. Justin Crocker  Is a corresponding author
  1. Janelia Farm Research Campus, Howard Hughes Medical Institute, United States
  2. European Molecular Biology Laboratory, Germany

Abstract

Transcription factors bind low-affinity DNA sequences for only short durations. It is not clear how brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) utilizes low-affinity binding sites in the Drosophila melanogaster shavenbaby (svb) locus and related enhancers in nuclear microenvironments of high Ubx concentrations. Related enhancers colocalize to the same microenvironments independently of their chromosomal location, suggesting that microenvironments are highly differentiated transcription domains. Manipulating the affinity of svb enhancers revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. The Ubx cofactor, Homothorax (Hth), was co-enriched with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. Thus, microenvironments of high local transcription factor and cofactor concentrations could help low-affinity sites overcome their kinetic inefficiency. Mechanisms that generate these microenvironments could be a general feature of eukaryotic transcriptional regulation.

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The following data sets were generated

Article and author information

Author details

  1. Albert Tsai

    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    tsaia@janelia.hhmi.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1643-0780
  2. Anand K Muthusamy

    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  3. Mariana RP Alves

    European Molecular Biology Laboratory, Heidelberg, Germany
    Competing interests
    No competing interests declared.
  4. Luke D Lavis

    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  5. Robert H Singer

    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    Robert H Singer, Reviewing editor, eLife.
  6. David L Stern

    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  7. Justin Crocker

    Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    justin.crocker@embl.de
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5113-0476

Funding

Damon Runyon Cancer Research Foundation (DRG 2220-15)

  • Albert Tsai

National Institutes of Health (U01-EB21236)

  • Robert H Singer

Howard Hughes Medical Institute

  • Albert Tsai
  • Anand K Muthusamy
  • Luke D Lavis
  • Robert H Singer
  • David L Stern
  • Justin Crocker

European Molecular Biology Laboratory

  • Mariana RP Alves
  • Justin Crocker

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

Reviewing Editor

  1. David N Arnosti, Michigan State University, United States

Version history

  1. Received: May 26, 2017
  2. Accepted: October 29, 2017
  3. Accepted Manuscript published: November 2, 2017 (version 1)
  4. Version of Record published: November 20, 2017 (version 2)

Copyright

© 2017, Tsai 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. Albert Tsai
  2. Anand K Muthusamy
  3. Mariana RP Alves
  4. Luke D Lavis
  5. Robert H Singer
  6. David L Stern
  7. Justin Crocker
(2017)
Nuclear microenvironments modulate transcription from low-affinity enhancers
eLife 6:e28975.
https://doi.org/10.7554/eLife.28975

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https://doi.org/10.7554/eLife.28975

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