1. Developmental Biology
  2. Chromosomes and Gene Expression
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Concentration dependent chromatin states induced by the bicoid morphogen gradient

  1. Colleen E Hannon
  2. Shelby A Blythe
  3. Eric F Wieschaus  Is a corresponding author
  1. Princeton University, United States
Research Article
  • Cited 23
  • Views 3,650
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Cite this article as: eLife 2017;6:e28275 doi: 10.7554/eLife.28275


In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset of its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations. This may be a common property of developmental transcription factors that must gain early access to their target enhancers while the chromatin state of the genome is being remodeled during large-scale transitions in the gene regulatory landscape.

Article and author information

Author details

  1. Colleen E Hannon

    Department of Molecular Biology, Princeton University, Princeton, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4402-8107
  2. Shelby A Blythe

    Department of Molecular Biology, Princeton University, Princeton, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Eric F Wieschaus

    Department of Molecular Biology, Princeton University, Princeton, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0727-3349


Howard Hughes Medical Institute

  • Eric F Wieschaus

National Institutes of Health (F31HD082940)

  • Colleen E Hannon

National Institutes of Health (F32HD072653)

  • Shelby A Blythe

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

Reviewing Editor

  1. Joaquín M Espinosa, University of Colorado School of Medicine, United States

Publication history

  1. Received: May 2, 2017
  2. Accepted: September 8, 2017
  3. Accepted Manuscript published: September 11, 2017 (version 1)
  4. Version of Record published: October 2, 2017 (version 2)


© 2017, Hannon 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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