Identification and characterization of the chromatin-binding domains of the HIV-1 integrase interactor LEDGF/p75

Depletion of the transcriptional co-activator LEDGF/p75 by RNA interference alters the genome-wide pattern of HIV-1 integration, reducing integration into active genes, reducing integration into LEDGF/p75-regulated genes, and increasing integration into G+C-rich sequences. LEDGF/p75 is also able to act as a molecular tether linking HIV-1 integrase protein to chromatin, a phenomenon likely to underlie the integration site distribution effects. The LEDGF/p75 integrase-binding domain has been established but the domain or domains responsible for the chromatin-binding component of tethering are unknown. Here, we identify and characterize these domains. Complementary methods were used to assess condensed and uncondensed chromatin, and to determine the stringency of chromatin binding. Immuno-localization analyses revealed that an N-terminal PWWP domain and its beta-barrel substructure are needed for binding to metaphase chromatin. However, the PWWP domain is insufficient to transfer metaphase chromatin binding to green fluorescent protein, which requires addition of a downstream charged region (CR1). Biochemical analysis showed that full-length LEDGF/p75 resists Triton X-100 extraction from chromatin. To transfer Triton-resistant chromatin binding to green fluorescent protein, PWWP-CR1 is necessary but not sufficient. Further inclusion of a tandem pair of AT-hooks in combination with at least one of two identified downstream charged regions (CR2 or CR3) is needed. Deletion of just the PWWP or the AT-hook domain from full-length LEDGF/p75 reduced Triton-resistant chromatin binding, while deletion of both elements abolished it, underscoring their dominant and cooperative role. The results establish a molecular mechanism for LEDGF/p75-mediated tethering of HIV-1 integrase to chromatin.