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A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide.
- Source :
-
ELife [Elife] 2021 Feb 23; Vol. 10. Date of Electronic Publication: 2021 Feb 23. - Publication Year :
- 2021
-
Abstract
- 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.<br />Competing Interests: PW No competing interests declared, KS Reviewing editor, eLife<br /> (© 2021, Wulfridge and Sarma.)
Details
- Language :
- English
- ISSN :
- 2050-084X
- Volume :
- 10
- Database :
- MEDLINE
- Journal :
- ELife
- Publication Type :
- Academic Journal
- Accession number :
- 33620319
- Full Text :
- https://doi.org/10.7554/eLife.65146