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

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. Sequencing data from E. coli MG1655 and S. cerevisiae. (i) E. coli GapR and GapR1-76 ChIP-seq, (ii) E. coli RNA-seq +/- GapR-3xFLAG expression, (iii) S. cerevisiae GapR ChIP-seq in raffinose +/- alpha-factor and in glycerol, (iv) S. cerevisiae RNA-seq +/- GapR, and (v) S. cerevisiae RNA-seq in raffinose +/- alpha-factor and in glycerol after GapR induction