Protocol for in vivo DNA-RNA hybrid immunoprecipitation, sequencing, and analysis from frozen mouse tissues
DNA-RNA hybrids (R-loops) form transiently on the genome and regulate cellular homeostasis. They also influence genome-editing outcomes, highlighting their therapeutic potential. Here, we present a protocol for high-resolution mapping of DNA-RNA hybrids from frozen mouse tissues, including genomic DNA extraction and isolation of digested DNA-RNA hybrids using the hybrid-specific S9.6 antibody. We detail procedures for processing hybrids for whole-genome sequencing to generate R-loop profiles. For details on the use of this protocol, please refer to Puzzo et al. 1
Authors
- Julia S. P. Mawer (ORCID: https://orcid.org/0000-0002-5207-3557)
- Magdalena P. Crossley (ORCID: https://orcid.org/0000-0002-8509-4645)
- Hassan Massalha (ORCID: https://orcid.org/0000-0002-9923-6878)
- Cameron Chee
- Francesco Puzzo (ORCID: https://orcid.org/0000-0001-9936-8873)
Institutions
- University of Cambridge (GB)
- Cancer Research UK (GB)
- Cancer Research UK Cambridge Center (GB)
- Telethon Institute Of Genetics And Medicine (IT)
Publication Details
- Journal
- STAR Protocols
- Published
- 2026-07-23
- DOI
- https://doi.org/10.1016/j.xpro.2026.104654
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Cancer Research UK