Systematic Evaluation of Different R-loop Mapping Methods: Achieving Consensus, Resolving Discrepancies and Uncovering Distinct Types of RNA:DNA Hybrids

Abstract

R-loop, a three-stranded nucleic acid structure, has been recognized to play pivotal roles in critical physiological and pathological processes. Multiple technologies have been developed to profile R-loops genome-wide, but the existing data suffer from major discrepancies on determining genuine R-loop localization and its biological functions. Here, we experimentally and computationally evaluate eight representative R-loop mapping technologies, and reveal inherent biases and artifacts of individual technologies as key sources of discrepancies. Analyzing signals detected with different R-loop mapping strategies, we note that genuine R-loops predominately form at gene promoter regions, whereas most signals in gene body likely result from structured RNAs as part of repeat-containing transcripts. Interestingly, our analysis also uncovers two classes of R-loops: The first class consists of typical R-loops where the single-stranded DNA binding protein RPA binds both the template and non-template strands. By contrast, the second class appears independent of Pol II-mediated transcription and is characterized by RPA binding only in the template strand. These two different classes of RNA:DNA hybrids in the genome suggest distinct biochemical activities involved in their formation and regulation. In sum, our findings will guide future use of suitable technology for specific experimental purposes and the interpretation of R-loop functions.

spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity

“…Different from R-ChIP, MapR, and CUT&Tag, spKAS-seq detects an appreciable level of RNA-DNA hybrids within gene bodies. This observation seems to corroborate DRIP-seq; however, recent findings suggest that most DRIP-seq signals within gene bodies appear to derive from dsRNA rather than R-loops (42,43). Note that the presence of spKAS-seq signals and their sensitivity to RNase H treatment indicate the presence of R-loops within gene bodies.…”