Journal
GENES & DEVELOPMENT
Volume 30, Issue 11, Pages 1327-1338Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gad.280834.116
Keywords
DNA:RNA hybrids; R loops; transcription; polyA tracts; RNase H
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Funding
- National Institutes of Health grant [R01 GM107583]
- Swiss National Science Foundation Advanced Postdoc.Mobility Fellowship
- Helen Hay Whitney Post-doctoral Fellowship
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R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA: RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA: RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae. Using this methodology, we identified similar to 800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast.
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