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Nucleic Acids Res. 2016 Sep 19;44(16):7830-47. doi: 10.1093/nar/gkw651. Epub 2016 Jul 20.

DNA minicircles clarify the specific role of DNA structure on retroviral integration.

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MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France.
Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France.
Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France.
Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France.
Institut Pasteur, PF1, Plate-forme Génomique-Pôle Biomics, Citech, Paris 75015, France.
Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR 5234 CNRS-Université de Bordeaux, Bordeaux 33000, France.
Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France


Chromatin regulates the selectivity of retroviral integration into the genome of infected cells. At the nucleosome level, both histones and DNA structure are involved in this regulation. We propose a strategy that allows to specifically study a single factor: the DNA distortion induced by the nucleosome. This strategy relies on mimicking this distortion using DNA minicircles (MCs) having a fixed rotational orientation of DNA curvature, coupled with atomic-resolution modeling. Contrasting MCs with linear DNA fragments having identical sequences enabled us to analyze the impact of DNA distortion on the efficiency and selectivity of integration. We observed a global enhancement of HIV-1 integration in MCs and an enrichment of integration sites in the outward-facing DNA major grooves. Both of these changes are favored by LEDGF/p75, revealing a new, histone-independent role of this integration cofactor. PFV integration is also enhanced in MCs, but is not associated with a periodic redistribution of integration sites, thus highlighting its distinct catalytic properties. MCs help to separate the roles of target DNA structure, histone modifications and integrase (IN) cofactors during retroviral integration and to reveal IN-specific regulation mechanisms.

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