title: DNA minicircles clarify the specific role of DNA structure on retroviral integration.
abstract: 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.
authors.affiliation: MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France.
authors.forename: Marco
authors.initials: M
authors.lastname: Pasi
authors.affiliation: Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France.
authors.forename: Damien
authors.initials: D
authors.lastname: Mornico
authors.affiliation: Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France.
authors.forename: Stevenn
authors.initials: S
authors.lastname: Volant
authors.affiliation: Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France.
authors.forename: Anna
authors.initials: A
authors.lastname: Juchet
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France.
authors.forename: Julien
authors.identifier: 0000-0003-1285-1083
authors.initials: J
authors.lastname: Batisse
authors.affiliation: Institut Pasteur, PF1, Plate-forme Génomique-Pôle Biomics, Citech, Paris 75015, France.
authors.forename: Christiane
authors.initials: C
authors.lastname: Bouchier
authors.affiliation: Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR 5234 CNRS-Université de Bordeaux, Bordeaux 33000, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Parissi
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Ruff
authors.affiliation: MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France.
authors.forename: Richard
authors.initials: R
authors.lastname: Lavery
authors.affiliation: Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France marc.lavigne@pasteur.fr.
authors.forename: Marc
authors.initials: M
authors.lastname: Lavigne
mesh_terms: D004270:DNA, Circular / Q000737:chemistry*; D004279:DNA, Viral / Q000737:chemistry*; D015723:Gene Library; D019427:HIV Integrase / Q000378:metabolism; D015497:HIV-1 / Q000502:physiology; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism; D012190:Retroviridae / Q000502:physiology*; D016662:Virus Integration
chemical_list: D004270:DNA, Circular; D004279:DNA, Viral; D036341:Intercellular Signaling Peptides and Proteins; D009707:Nucleosomes; C119380:lens epithelium-derived growth factor; D019427:HIV Integrase