1. Developmental Biology and Stem Cells
  2. Genes and Chromosomes
Download icon

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
0
Views
940
Comments
0
Cite as: eLife 2017;6:e28275 doi: 10.7554/eLife.28275

Abstract

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 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
    efw@princeton.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon 0000-0002-0727-3349

Funding

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, Reviewing Editor, 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)

Copyright

© 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.

Metrics

  • 940
    Page views
  • 252
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: PubMed Central, Scopus, Crossref.

Comments

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)

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

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