I-104 Distinct chromosomal positions of intact HIV-1 proviruses

Abstract

A small reservoir of chromosomally-integrated, genome-intact but transcriptionally-silent HIV-1 proviruses persists lifelong despite suppressive antiretroviral therapy, and makes HIV-1 infection an incurable disease. Yet, very little is known about the positions of such intact proviruses in the human genome, or the mechanisms that contribute to maintaining their transcriptional latency. Here, we used a novel experimental approach involving multiple displacement amplification of individual HIV-1 proviral species, followed by near full-length HIV-1 next-generation sequencing and corresponding chromosomal integration site analysis to selectively map the chromosomal positions of intact HIV-1 proviruses in 3 HIV-1-infected individuals undergoing long-term antiretroviral therapy. We observed that in comparison to defective proviral sequences, intact HIV-1 proviruses were enriched for non-genic chromosomal positions and more frequently displayed an opposite orientation relative to host genes. In addition, intact HIV-1 proviruses were preferentially integrated either in relative proximity or in increased distance to active transcriptional start sites and to accessible chromatin regions. These studies strongly suggest selection of intact proviruses with features of deeper viral latency during prolonged antiretroviral therapy, and may be important for developing targeted strategies to purge the genome-intact viral reservoir.