Intasome architecture and chromatin density modulate retroviral integration into nucleosome

Abstract

BackgroundRetroviral integration depends on the interaction between intasomes, host chromatin and cellular targeting cofactors as LEDGF/p75 or BET proteins. Previous studies indicated that the retroviral integrase, by itself, may play a role in the local integration site selection within nucleosomal target DNA. We focused our study on this local association by analyzing the intrinsic properties of various retroviral intasomes to functionally accommodate different chromatin structures in the lack of other cofactors.ResultsUsing in vitro conditions allowing the efficient catalysis of full site integration without these cofactors, we show that distinct retroviral integrases are not equally affected by chromatin compactness. Indeed, while PFV and MLV integration reactions are favored into dense and stable nucleosomes, HIV-1 and ASV concerted integration reactions are preferred into poorly dense chromatin regions of our nucleosomal acceptor templates. Predicted nucleosome occupancy around integration sites identified in infected cells suggests the presence of a nucleosome at the MLV and HIV-1 integration sites surrounded by differently dense chromatin. Further analyses of the relationships between the in vitro integration site selectivity and the structure of the inserted DNA indicate that structural constraints within intasomes could account for their ability to accommodate nucleosomal DNA and could dictate their capability to bind nucleosomes functionally in these specific chromatin contexts.ConclusionsThus, both intasome architecture and compactness of the chromatin surrounding the targeted nucleosome appear important determinants of the retroviral integration site selectivity. This supports a mechanism involving a global targeting of the intasomes toward suitable chromatin regions followed by a local integration site selection modulated by the intrinsic structural constraints of the intasomes governing the target DNA bending and dictating their sensitivity toward suitable specific nucleosomal structures and density.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-015-0145-9) contains supplementary material, which is available to authorized users.

Retroviral DNA Integration

“…156 It remains a mystery if and how IN signals completion of strand transfer for recruitment of STC disassembly and DNA repair machineries. Given the apparent preference of retroviruses to integrate into nucleosomes, 191,194,197 chromatin remodellers appear to be good candidates for the job of STC disassembly.…”

Different Pathways Leading to Integrase Inhibitors Resistance

“…ST reaction, performed preferentially by a dimer of IN, corresponds to the integration of one DNA extremity. This half-site ST reaction can be easily recorded in vitro using ODN or long substrate DNA (Sinha et al, 2002; Sinha and Grandgenett, 2005; Li et al, 2006; Benleulmi et al, 2015). Concerted integration involves the integration of two viral DNA extremities in the same location leading to the 5-bp duplication (in the case of HIV-1) of the sequence flanking the integration site, and is catalyzed by a tetramer of IN (dimer of dimer) (Lesbats et al, 2008; Benleulmi et al, 2015).…”

“…This half-site ST reaction can be easily recorded in vitro using ODN or long substrate DNA (Sinha et al, 2002; Sinha and Grandgenett, 2005; Li et al, 2006; Benleulmi et al, 2015). Concerted integration involves the integration of two viral DNA extremities in the same location leading to the 5-bp duplication (in the case of HIV-1) of the sequence flanking the integration site, and is catalyzed by a tetramer of IN (dimer of dimer) (Lesbats et al, 2008; Benleulmi et al, 2015). This overall process actually corresponds to the full-site integration process that occurs in vivo and can be performed in vitro by recombinant IN and purified PIC (Faure et al, 2005; Sinha and Grandgenett, 2005).…”

Retroviral Integrase: Then and Now

“…Finally, the betaretrovirus mouse mammary tumor virus (MMTV) exhibits no significant deviation from random in integration site preference. Dissimilar requirements for chromatin structure or accessibility may explain some of these differences (46–48). In at least two cases, it is now clear that attachment to specific chromatin protein tethers is a major determinant for integration site selection: A loop in a C-terminal domain of the chromatin-targeting transcription factor lens epithelium–derived growth factor (LEDGF/p75) binds tightly in a pocket formed at a dimer interface of HIV-1 IN, and the conserved extraterminal domain of Brd proteins, commonly found in transcriptional promoter regions, attaches to a short sequence in the C-terminal tail of the MLV and feline leukemia virus (FeLV) IN proteins (49–52).…”