Functional interactions between retroviral integration complexes and host chromatin unveiled

Functional interactions between retroviral integration complexes and host chromatin unveiled

The cell infection by a retrovirus requires the stable insertion of the viral genome into the host chromosomes catalyzed by the viral DNA/integrase complex called intasome. This process is regulated by multiple factors as the nuclear entry pathway, nucleus architecture, chromatin state and the intasome targeting by cellular tethering proteins. One key steps in the integration mechanism is the final association between the incoming intasome and the nucleosome. Our work has been focused for several years on studying this functional association.

Biochemical integration assays on various reconstituted chromatin templates with various recombinant integrases from different retroviruses genera were set up in the team. Using this model, we have demonstrated that the different intasomes were not equally sensitive to the chromatin structure. While the nucleosome is a good substrate for integration Lentiviral (HIV-1) and alpha-retroviral (ASV) INs were found inhibited by chromatin compaction and spumaviral (PFV) and gamma-retroviral (MLV) INs were found to accommodate more easily the different chromatin structures with a significant preference for compact chromatin. Taken together these data led us to conclude that both the structure of the intasomes and the chromatin surrounding the targeted nucleosome regulate retroviral integration into the host genome (1). Our data also suggested that additional contacts between the intasome and the nucleosome, masked during chromatin compaction, could be required for efficient HIV-1 integration. This was supported by the recent demonstration of a direct interaction between HIV-1 IN and histone tails, especially histone H4 tail, and its role in regulating integration both in vitro and in vivo (2). These IN/histone interactions can be modulated by the structure of the chromatin, as previously suggested by the coupling found between integration and cellular chromatin remodeling activity (3). Further proteomic approaches led us to select the histone chaperon FACT as a new integration factor that modulates the access of the nucleosome for the incoming intasome by remodeling the chromatin in the polII transcribed genes regions targeted by HIV-1 (4). Our work provides new information about the process of target DNA capture by the retroviral integration complexes and unveils new host/pathogens interactions. These interactions may constitute bases for the development of new antiviral approaches as well as optimized gene therapy strategies using retroviral vectors.

This four years project has been supported by ANR, ANRS and SIDACTION and gave birth to a strong collaborative network DyNAVir (Viral DNA integration and chromatin dynamics) coordinated by our team and including experts in proteins structures determination, chromatin, retroviruses infection/integration and gene therapy: M. Ruff (IGBMC, strasbourg), P. Gouet, X. Robert (IBCP, Lyon), O. Delelis (LBPA, ENS Cachan), Z. Ivics (PEI Hamburg).

1. Benleulmi MS, Matysiak J, Henriquez DR, Vaillant C, Lesbats P, Calmels C, Naughtin M, Leon O, Skalka AM, Ruff M, Lavigne M, Andreola ML, Parissi V. 2015. Intasome architecture and chromatin density modulate retroviral integration into nucleosome. Retrovirology 12:13.

2. Benleulmi MS, Matysiak J, Robert X, Miskey C, Mauro E, Lapaillerie D, Lesbats P, Chaignepain S, Henriquez DR, Calmels C, Oladosu O, Thierry E, Leon O, Lavigne M, Andreola M-L, Delelis O, Ivics Z, Ruff M, Gouet P, Parissi V. 2017. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails. Retrovirology 14:54.

3. Lesbats P, Botbol Y, Chevereau G, Vaillant C, Calmels C, Arneodo A, Andreola ML, Lavigne M, Parissi V. 2011. Functional Coupling between HIV-1 Integrase and the SWI/SNF Chromatin Remodeling Complex for Efficient in vitro Integration into Stable Nucleosomes. PLoS Pathog 7:e1001280.

4. Matysiak J, Lesbats P, Mauro E, Lapaillerie D, Dupuy J-W, Lopez AP, Benleulmi MS, Calmels C, Andreola M-L, Ruff M, Llano M, Delelis O, Lavigne M, Parissi V. 2017. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration. Retrovirology 14.

 
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