Mapping HIV-1 RNA structure, homodimers, long-range interactions and persistent domains by HiCapR.

ABSTRACT: Human Immunodeficiency Virus type 1 (HIV-1) RNA genome organization remains a critical knowledge gap in understanding its replication cycle. To address this, we developed HiCapR, a psoralen crosslinking-based RNA proximity ligation method coupled with post-library hybridization, enabling high-resolution mapping of RNA-RNA interactions across the HIV-1 genome. This approach confirmed canonical structural motifs, including stem-loop architectures in the 5'-untranslated region (5'-UTR) and Rev Response Element (RRE), as well as dimerization sites within the 5'-UTR critical for viral packaging. Notably, HiCapR identified novel homodimerization events distributed along the genome, suggesting an expanded regulatory role of RNA multimerization in splicing regulation and selective encapsidation. I

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC12180898 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature