Direct RNA-Mediated Epigenetic Silencing of Innate Immune Genes by HIV-1: Integrated Mechanistic and Clinical Evidence

Background HIV-1 establishes persistent infection through complex epigenetic manipulation of host immune responses. While viral protein-mediated mechanisms are well characterized, the direct involvement of HIV-1-derived RNAs in epigenetic regulation remains incompletely understood. Methods We employed an integrated approach combining DNA:RNA hybrid immunoprecipitation (DRIP-qPCR), chromatin isolation by RNA purification sequencing (ChIRP-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) in primary CD4 + T cells with clinical transcriptomic profiling of 105 participants (50 chronic HIV-1 patients, 30 long-term non-progressors, and 25 healthy controls). Results HIV-1 infection induced significant RNA-DNA hybrid formation at promoters of key innate immune genes, including IFNG (mean fold enrichment: 4.65, 95% CI: 4.2–5.1, p < 0.001), IL2 (mean: 4.2, 95% CI: 3.9–4.5, p < 0.001), and CXCL10 (mean: 4.45, 95% CI: 4.1–4.8, p < 0.001). ChIRP-seq identified 134 high-confidence chromatin regions interacting with HIV-1 LTR RNA (FDR < 0.01). ChIP-seq revealed increased H3K27me3 deposition and EZH2 recruitment at these loci. Clinical validation demonstrated significant downregulation of immune genes in chronic patients versus LTNPs, with H3K27me3 levels positively correlating with viral load (β = 0.79, 95% CI: 0.68–0.90, p < 0.001). Conclusion Our findings support a model where HIV-1-derived RNA contributes to epigenetic repression of innate immune genes through R-loop-associated mechanisms, complementing established protein-mediated pathways of immune evasion.