Aquarius helicase facilitates HIV-1 Integration into R-loop enriched genomic regions

The integration of HIV-1 is a pivotal step in the viral life cycle, facilitating the stable insertion of the viral DNA genome into host chromosomes. This process significantly influences subsequent infection stages, including viral transcription and the establishment of latent reservoirs. The viral integrase (IN) plays a crucial role in this process and with cellular cofactor LEDGF/p75 targets recurrently intragenic regions of transcriptionally active genes. However, many aspects of recurrent genic targeting of active genes remain obscure, and the genomic determinants of HIV-1 integration are still missing. We show that HIV-1 genic integrations occur in the proximity of R-loops, RNA:DNA hybrids formed predominantly in intronic regions of active genes in primary activated CD4+ T cells. In order to integrate into these dynamic genomic structures, HIV-1 Integrase requires a co-factor, which we identify to be a splicing helicase Aquarius (AQR), within the Intron Binding Complex (IBC). We show that AQR's role in unwinding RNA:DNA hybrids promotes integration into R-loop-rich genomic regions. Our discovery puts the RNA component of the cellular chromatin into the limelight and indicates that the interaction of HIV-1 IN with RNA might play a pivotal role in drug targeting.