1. Chromosomes and Gene Expression
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High-resolution, genome-wide mapping of positive supercoiling in chromosomes

  1. Monica S Guo  Is a corresponding author
  2. Ryo Kawamura
  3. Megan L Littlehale
  4. John F Marko
  5. Michael T Laub  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
  2. Northwestern University, United States
Research Article
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Cite this article as: eLife 2021;10:e67236 doi: 10.7554/eLife.67236

Abstract

Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently-oriented genes, consistent with the 'twin-domain' model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

Data availability

Datasets generated during this study are deposited at the Gene Expression Omnibus (GEO): GSE152882.

The following data sets were generated

Article and author information

Author details

  1. Monica S Guo

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    msguo@mit.edu
    Competing interests
    No competing interests declared.
  2. Ryo Kawamura

    Department of Molecular Biosciences, Northwestern University, Evanston, United States
    Competing interests
    No competing interests declared.
  3. Megan L Littlehale

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.
  4. John F Marko

    Department of Molecular Biosciences, Department of Physics and Astronomy, Northwestern University, Evanston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4151-9530
  5. Michael T Laub

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    laub@mit.edu
    Competing interests
    Michael T Laub, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8288-7607

Funding

National Institutes of Health (K99GM134153)

  • Monica S Guo

National Institutes of Health (U54CA193419)

  • John F Marko

National Institutes of Health (U54DK107980)

  • John F Marko

National Institutes of Health (R01GM082899)

  • Michael T Laub

National Institutes of Health (S10OD026741)

  • Monica S Guo

Howard Hughes Medical Institute (Investigator)

  • Michael T Laub

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

Reviewing Editor

  1. James M Berger, Johns Hopkins University School of Medicine, United States

Publication history

  1. Received: February 4, 2021
  2. Accepted: July 16, 2021
  3. Accepted Manuscript published: July 19, 2021 (version 1)

Copyright

© 2021, Guo 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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