Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails

Abstract

BackgroundStable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein–protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process.ResultsWe show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy.ConclusionsCollectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin.Electronic supplementary materialThe online version of this article (10.1186/s12977-017-0378-x) contains supplementary material, which is available to authorized users.

Human H4 tail stimulates HIV-1 integration through binding to the carboxy-terminal domain of integrase

“…Taken together, these data suggest that specific intasome/nucleosome contacts are required for optimal integration and may be regulated by chromatin compaction and remodelling. This hypothesis is further supported by the demonstration of direct IN/histone interactions in the solved cryoEM structure of the PFV intasome/nucleosome (9) and the recent finding of the direct binding of HIV-1 IN to histone tails, especially histone 4 (H4), promoting nucleosomal integration (17). In both cases the interactions between INs and histones occur via the carboxy-terminal domains (CTD) of the retroviral enzymes.…”

“…In both cases the interactions between INs and histones occur via the carboxy-terminal domains (CTD) of the retroviral enzymes. Moreover, mutations in the CTD of the INs that impair their binding to histones also impair their functional association with the nucleosomes as well as cellular integration efficiency and selectivity providing biological evidence for the relevance of the IN/histone interaction (9,17).…”

The chromatin landscape at the HIV-1 provirus integration site determines viral expression

“…Additionally, HIV IN itself might affect integration site selection as it shows a weak preference for a conserved sequence logo at the site of integration ( 107–109 ). Moreover, HIV IN was shown to directly interact with chromatin via interaction with H4 amino-terminal tails ( 110 ).…”

Impact of LEDGIN treatment during virus production on residual HIV-1 transcription

“…Moreover, LEDGIN treatment during virus production enhances IN oligomerization prematurely in the viral particle, and these multimers are retained in the cytoplasm and nucleus after infection of target cells [64,94]. Although enhanced/premature IN oligomerization may not affect targeting by LEDGF/p75, it might still influence in which chromatin environment integration takes place, for instance by a direct interaction between IN and histone amino-terminal tails [49]. The exact mechanism remains to be clarified.…”

“…Active genes are characterized by an open chromatin landscape and specific epigenetic histone modifications such as H3K36me3, the recognition mark of LEDGF/p75 [46][47][48]. Moreover, it was recently found that HIV IN directly interacts with the amino-terminal tail of histone H4, which promotes its anchoring to the nucleosome and facilitates integration [49]. Additionally, HIV IN shows a weak preference for a conserved sequence logo at the site of integration [50][51][52].…”