1. Chromosomes and Gene Expression
  2. Genetics and Genomics
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Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo

  1. Michael R Stadler
  2. Jenna E Haines
  3. Michael Eisen  Is a corresponding author
  1. University of California, Berkeley, United States
Research Article
  • Cited 25
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Cite this article as: eLife 2017;6:e29550 doi: 10.7554/eLife.29550

Abstract

High-throughput assays of three-dimensional interactions of chromosomes have shed considerable light on the structure of animal chromatin. Despite this progress, the precise physical nature of observed structures and the forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate that boundaries between topological domains of various sizes map to DNA elements that resemble classical insulator elements: short genomic regions sensitive to DNase digestion that are strongly bound by known insulator proteins and are frequently located between divergent promoters. Further, we show a striking correspondence between these elements and the locations of mapped polytene interband regions. We believe it is likely this relationship between insulators, topological boundaries, and polytene interbands extends across the genome, and we therefore propose a model in which decompaction of boundary-insulator-interband regions drives the organization of interphase chromosomes by creating stable physical separation between adjacent domains.

Article and author information

Author details

  1. Michael R Stadler

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3333-4184
  2. Jenna E Haines

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Michael Eisen

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    mbeisen@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7528-738X

Funding

Howard Hughes Medical Institute

  • Michael Eisen

American Cancer Society

  • Michael R Stadler

National Science Foundation

  • Jenna E Haines

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

Reviewing Editor

  1. Allan C Spradling, Howard Hughes Medical Institute, Carnegie Institution for Science, United States

Publication history

  1. Received: June 13, 2017
  2. Accepted: November 13, 2017
  3. Accepted Manuscript published: November 17, 2017 (version 1)
  4. Version of Record published: December 21, 2017 (version 2)

Copyright

© 2017, Stadler 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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