Human immunodeficiency virus-1 induces and targets host genomic R-loops for viral genome integration

Although HIV-1 integration sites are considered to favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites have shown that the virus can integrate in a variety of host genomic locations, including non-genic regions. The invisible infection by HIV-1 integrating into non-genic regions challenging the traditional understanding of HIV-1 integration site selection are rather more problematic as they are selected to preserve in the host genome during prolonged antiretroviral therapies. Here, we showed that HIV-1 targets R-loops, a genomic structure made up of DNA–RNA hybrids, for integration. HIV-1 initiates the formation of R-loops in both genic and non-genic regions of the host genome and preferentially integrates into R-loop-rich regions. Using a cell model that can independently control transcriptional activity and R-loop formation, we demonstrated that the formation of R-loops directs HIV-1 integration targeting sites. We also found that HIV-1 integrase proteins physically bind to the host genomic R-loops. These findings provide fundamental insights into the mechanisms of retroviral integration and the new strategies of antiretroviral therapy against HIV-1 latent infection.