High-resolution, genome-wide mapping of positive supercoiling in chromosomes
Name
elife-67236-v1.pdf
Description
Published version
Size
20.69 MB
Format
Adobe PDF
Checksum (MD5)
d75a504701fe36297b75312373a3d4ab
Author(s)
Guo, Monica S
Kawamura, Ryo
Littlehale, Megan L
Marko, John F
Laub, Michael T
Date Issued
July 19, 2021
Journal
eLife
Publisher
eLife Sciences Publications, Ltd
Version
Final published version
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 Escherichia coli and Saccharomyces 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.
MIT Department
Massachusetts Institute of Technology. Department of Biology
Howard Hughes Medical Institute
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.7554/elife.67236
