Relationship between the distribution of LEDGF along genes and positions of HIV-1 DNA integration

ABSTRACT HIV-1 integration occurs across actively transcribed genes due to the interaction of integrase (IN) with LEDGF, a host factor. Although LEDGF was originally isolated as a co-activator that stimulates promoter activity in purified systems, this activity appears inconsistent with LEDGF-mediated integration across genes and with data indicating that LEDGF promotes transcriptional elongation. We found LEDGF was enriched in peaks that match the enrichments of H3K4me3 and RNA Pol II at transcription start sites (TSSs) of active promoters. LEDGF harbors two globular domains, a Pro-Trp-Trp-Pro (PWWP) chromatin reader with specificity for H3K36me3, and an IN binding domain (IBD) that mediates interactions with IN and numerous cellular factors including MLL1. The IBD and MLL1 mediated LEDGF recruitment to promoters. In turn, LEDGF promoted the association of RNA Pol II at TSSs. Consistent with greater enrichment of H3K36me3 at the 3′ regions of genes, LEDGF lacking the PWWP domain had reduced association with downstream sequences and increased enrichment at TSSs. HIV-1 integration levels per gene revealed that a threshold amount of LEDGF at TSSs was associated with integration in downstream sequence. It is thought that the PWWP domain and the enrichment of H3K36me3 in transcribed sequences are responsible for integration across genes. Although the distribution of HIV-1 integrations across gene bodies was shifted upstream in cells lacking H3K36me3, integration levels per gene were unchanged. Our results support a model where LEDGF is tethered to promoters via IBD-mediated cell factor interactions. Subsequently, LEDGF associates with RNA Pol II during elongation to effect HIV-1 integration site targeting. IMPORTANCE Over 40 million people are currently infected with HIV-1, and approximately one million new infections occur each year. While antiretroviral drugs are extremely successful in suppressing HIV-1, drug resistance is increasing, and there are no reasonable approaches to cure patients of the virus. The chromatin-associated transcription factor LEDGF interacts directly with viral integrase (IN), causing HIV-1 integration to occur across the bodies of actively transcribed genes. The research here identifies the molecular determinants that position LEDGF at promoters and across genes. Our experiments discovered that LEDGF at promoters does not mediate integration. These results may lead to the identification of factors and interactions that inhibit integration and offer the potential to develop antiviral therapies that suppress HIV-1 replication.*Corresponding author