Rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo.

ABSTRACT: HIV-1 integration favors recurrent integration gene (RIG) targets and genic proviruses can confer cell survival in vivo. However, the relationship between initial RIG integrants and how these evolve in patients over time are unknown. To address these shortcomings, we built phenomenological models of random integration in silico, which were used to identify 3718 RIGs as well as 2150 recurrent avoided genes from 1.7 million integration sites across 10 in vitro datasets. Despite RIGs comprising only 13% of human genes, they harbored 70% of genic HIV-1 integrations across in vitro and patient-derived datasets. Although previously reported to associate with super-enhancers, RIGs tracked more strongly with speckle-associated domains. While depletion of the integrase cofactor LEDGF/p75 significan

SUBMITTER: Bedwell GJ 

PROVIDER: S-EPMC8287940 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature