High-resolution, genome-wide mapping of positive supercoiling in chromosomes
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.
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High-resolution, genome-wide mapping of positive supercoiling in chromosomesNCBI Gene Expression Omnibux, GSE152882.
Article and author information
Author details
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
- James M Berger, Johns Hopkins University School of Medicine, United States
Version history
- Received: February 4, 2021
- Preprint posted: February 25, 2021 (view preprint)
- Accepted: July 16, 2021
- Accepted Manuscript published: July 19, 2021 (version 1)
- Version of Record published: August 12, 2021 (version 2)
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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