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

eLife

Monica S Guo¹  Megan L Littlehale¹  Michael T Laub²  Ryo Kawamura³  John F Marko⁴ 

[1] Department of Biology, Massachusetts Institute of Technology, Cambridge, United States;Department of Biology, Massachusetts Institute of Technology, Cambridge, United States;Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States;Department of Molecular Biosciences, Northwestern University, Evanston, United States;Department of Molecular Biosciences, Northwestern University, Evanston, United States;Department of Physics and Astronomy, Northwestern University, Evanston, United States;

关键词: supercoiling;    chromosome structure;    gene expression;    E. coli;    S. cerevisiae;   

DOI  :  10.7554/eLife.67236

来源: eLife Sciences Publications, Ltd

【 摘 要 】

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.

【 授权许可】

CC BY