High-Resolution Mapping of RNA-RNA Interactions Across the HIV-1 Genome With HicapR
Haobo Wang1, Yan Zhang1, Jingwan Han2
1Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, China.
Bio-Protocol
|June 29, 2026
Summary
HiCapR is a new protocol that precisely maps viral RNA structures, revealing functional domains and interactions crucial for virus infection and antiviral development.
Area of Science:
- Virology
- Molecular Biology
- Genomics
Background:
- Viral RNA genomes form dynamic structures essential for infection and immune evasion.
- Existing genome-wide RNA interaction mapping methods lack specificity for low-abundance targets in complex samples.
Purpose of the Study:
- To develop a highly specific and efficient protocol for capturing and analyzing viral RNA-RNA interactions.
- To generate high-resolution RNA interaction maps for viral genomes.
Main Methods:
- HiCapR protocol integrates in vivo psoralen crosslinking, RNA fragmentation, proximity ligation, and hybridization capture.
- Captured libraries are sequenced and analyzed using a custom computational pipeline to reconstruct RNA secondary structures.
Main Results:
- HiCapR successfully resolved the in vivo structure of the HIV-1 RNA genome, identifying functional domains, homodimers, and long-range interactions.
- The protocol demonstrated robustness on SARS-CoV-2 and efficiently captures low-abundance RNA from complex samples.
Conclusions:
- HiCapR provides an efficient and specific tool for studying viral RNA architecture, combining proximity ligation with targeted enrichment.
- This method offers broad applications in virology research and the development of antiviral therapies.
