High-resolution, genome-wide mapping of positive supercoiling in chromosomes

Abstract
Data availability
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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

1. Guo MS
2. Laub MT
(2021) High-resolution, genome-wide mapping of positive supercoiling in chromosomes
NCBI Gene Expression Omnibux, GSE152882.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152882

Article and author information

Author details

Monica S Guo

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States

For correspondence
msguo@mit.edu

Competing interests
No competing interests declared.
Ryo Kawamura

Department of Molecular Biosciences, Northwestern University, Evanston, United States

Competing interests
No competing interests declared.
Megan L Littlehale

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
No competing interests declared.
John F Marko

Department of Molecular Biosciences, Department of Physics and Astronomy, Northwestern University, Evanston, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-4151-9530
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.

"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.

Copyright

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.