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Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach.

ABSTRACT: R-loops are three-stranded DNA:RNA hybrids that are implicated in many nuclear processes. While R-loops may have physiological roles, the formation of stable, aberrant R-loops has been observed in neurological disorders and cancers. Current methods to assess their genome-wide distribution rely on affinity purification, which is plagued by large input requirements, high noise, and poor sensitivity for dynamic R-loops. Here, we present MapR, a method that utilizes RNase H to guide micrococcal nuclease to R-loops, which are subsequently cleaved, released, and identified by sequencing. MapR detects R-loops formed at promoters and active enhancers that are likely to form transient R-loops due to the low transcriptional output of these regulatory elements and the short-lived nature of enhancer RNAs. MapR is as specific as existing techniques and more sensitive, allowing for genome-wide coverage with low input material in a fraction of the time.

SUBMITTER: Yan Q

PROVIDER: S-EPMC6870988 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach.

Yan Qingqing Q Shields Emily J EJ Bonasio Roberto R Sarma Kavitha K

Cell reports 20191001 5

R-loops are three-stranded DNA:RNA hybrids that are implicated in many nuclear processes. While R-loops may have physiological roles, the formation of stable, aberrant R-loops has been observed in neurological disorders and cancers. Current methods to assess their genome-wide distribution rely on affinity purification, which is plagued by large input requirements, high noise, and poor sensitivity for dynamic R-loops. Here, we present MapR, a method that utilizes RNase H to guide micrococcal nucl ...[more]

PMID: 31665646

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