MapR: A Method for Identifying Native R‐Loops Genome Wide

R‐loops are abundant, RNA‐containing chromatin structures that form in the genomes of both eukaryotes and prokaryotes. Devising methods to identify the precise genomic locations of R‐loops is critical to understand how these structures regulate numerous cellular processes, including replication, termination, and chromosome segregation, and how their unscheduled formation results in disease. Here, we describe a new, highly sensitive, and antibody‐independent method, MapR, to profile native R‐loops genome wide. MapR takes advantage of the natural specificity of the RNase H enzyme to recognize DNA:RNA hybrids, a defining feature of R‐loops, and combines it with a CUT&RUN approach to target, cleave, and release R‐loops that can then be sequenced. MapR has low background, is faster than current R‐loop detection technologies, and can be performed in any cell type without the need to generate stable cell lines. © 2020 by John Wiley & Sons, Inc.