TY - JOUR TI - A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide AU - Wulfridge, Phillip AU - Sarma, Kavitha A2 - Chang, Howard Y A2 - Struhl, Kevin A2 - Chang, Howard Y VL - 10 PY - 2021 DA - 2021/02/23 SP - e65146 C1 - eLife 2021;10:e65146 DO - 10.7554/eLife.65146 UR - https://doi.org/10.7554/eLife.65146 AB - R-loops are three-stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation is associated with genome instability and is observed in neurodevelopmental diseases and cancers. Genome-wide profiling of R-loops in normal and diseased cells can help identify locations of pathogenic R-loops and advance efforts to attenuate them. We present an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce genome-wide profiles that retain strand information. BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. In mouse embryonic stem cells, we apply BisMapR to find that gene promoters form R-loops in both directions and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression. KW - R-loops KW - enhancers KW - strand-specific KW - genome-wide JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -