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.

Highlights

  • Retroviral integration depends on the interaction between intasomes, host chromatin and cellular targeting cofactors as LEDGF/p75 or bromodomain and extraterminal domain (BET) proteins

  • Numerous partial structures of INs from different retroviral genera have been determined, only prototype foamy virus (PFV) IN has been crystallized in its full-length form, in the presence of its DNA substrates, providing unprecedented details on the organization of the successive nucleoprotein complexes involved in the integration process, from the stable synaptic complex (SSC, referred to as the intasome) to the strand transfer complex (STC) [8,9,10]

  • In vitro integration catalyzed on chromatin by integrases from various retroviral genera human immunodeficience virus (HIV)-1, PFV, murine leukemia virus (MLV) and avian sarcoma virus (ASV) INs were compared using their specific donor DNAs and p5S acceptor plasmids derived from the previously described pBSK-Zeo-S5G5E4 receptor vector (Figure 1A and Additional file 2: Figure S2A) containing a 5S-G5E4 fragment carrying two times five repeats of 5S sequences surrounding a central sequence containing five gal4 DNA binding sites and the adenovirus 2 E4 minimal promoter

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Summary

Introduction

Retroviral integration depends on the interaction between intasomes, host chromatin and cellular targeting cofactors as LEDGF/p75 or BET proteins. Numerous partial structures of INs from different retroviral genera have been determined, only PFV IN has been crystallized in its full-length form, in the presence of its DNA substrates, providing unprecedented details on the organization of the successive nucleoprotein complexes involved in the integration process, from the stable synaptic complex (SSC, referred to as the intasome) to the strand transfer complex (STC) [8,9,10] In agreement with these structural data, previous biochemical studies performed on INs from different retroviruses have concluded that the integration reaction was carried out by an IN tetramer [13,14,15], the global architecture of the intasome and the STC might vary from a system to another [16,17]. Some post-translational modifications of HIV-1 IN have been reported that could affect the enzyme activity and its cellular behavior [19,20]

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