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High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-Seq 2]

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 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 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, replication-transcription encounters, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach that can be applied in any organism to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE164186 | GEO | 2021/06/25

REPOSITORIES: GEO

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

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High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-seq]

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