title: DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity.
abstract: Retroviral integrases (INs) catalyse the integration of the reverse transcribed viral DNA into the host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in the viral life cycle. However, the precise underlying mechanisms are still under investigation. We have developed a new in vitro integration assay using physiologically-relevant, reconstituted genomic acceptor chromatin and high-throughput determination of nucleosome positions and integration sites, in parallel. A quantitative analysis of the resulting data reveals a chromatin-dependent redistribution of the integration sites and establishes a link between integration sites and nucleosome positions. The co-activator LEDGF/p75 enhanced integration but did not modify the integration sites under these conditions. We also conducted an in cellulo genome-wide comparative study of nucleosome positions and human immunodeficiency virus type-1 (HIV-1) integration sites identified experimentally in vivo. These studies confirm a preferential integration in nucleosome-covered regions. Using a DNA mechanical energy model, we show that the physical properties of DNA probed by IN binding are important in determining IN selectivity. These novel in vitro and in vivo approaches confirm that IN has a preference for integration into a nucleosome, and suggest the existence of two levels of IN selectivity. The first depends on the physical properties of the target DNA and notably, the energy required to fit DNA into the IN catalytic pocket. The second depends on the DNA deformation associated with DNA wrapping around a nucleosome. Taken together, these results indicate that HIV-1 IN is a shape-readout DNA binding protein.
authors.affiliation: Laboratoire Joliot-Curie, CNRS USR 3010, Ecole Normale Supérieure, Lyon, France.
authors.forename: Monica
authors.initials: M
authors.lastname: Naughtin
authors.affiliation: Laboratoire Joliot-Curie, CNRS USR 3010, Ecole Normale Supérieure, Lyon, France.
authors.forename: Zofia
authors.initials: Z
authors.lastname: Haftek-Terreau
authors.affiliation: Laboratoire Joliot-Curie, CNRS USR 3010, Ecole Normale Supérieure, Lyon, France.
authors.forename: Johan
authors.initials: J
authors.lastname: Xavier
authors.affiliation: Université de Lyon, Microbiologie Adaptation et Pathogénie, INSA Lyon, CNRS UMR 5240, Lyon, France.
authors.forename: Sam
authors.initials: S
authors.lastname: Meyer
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR9198, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.
authors.forename: Maud
authors.initials: M
authors.lastname: Silvain
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR9198, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France.
authors.forename: Yan
authors.initials: Y
authors.lastname: Jaszczyszyn
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale Intégrative, UDS, CNRS UMR 7104-INSERM U 964, Illkirch, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Levy
authors.affiliation: Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon1, Lyon, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Miele
authors.affiliation: Laboratoire Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Université Victor Segalen Bordeaux 2, Bordeaux, France.
authors.forename: Mohamed Salah
authors.initials: MS
authors.lastname: Benleulmi
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie Structurale Intégrative, UDS, CNRS UMR 7104-INSERM U 964, Illkirch, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Ruff
authors.affiliation: Laboratoire Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Université Victor Segalen Bordeaux 2, Bordeaux, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Parissi
authors.affiliation: Laboratoire du Physique, CNRS UMR 5672, Ecole Normale Supérieure, Lyon, France.
authors.forename: Cédric
authors.initials: C
authors.lastname: Vaillant
authors.affiliation: Laboratoire Joliot-Curie, CNRS USR 3010, Ecole Normale Supérieure, Lyon, France; Institut Pasteur, Dpt de Virologie, UMR 3569 CNRS, Paris, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Lavigne
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000378:metabolism; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D019427:HIV Integrase / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D011485:Protein Binding; D013379:Substrate Specificity; D016662:Virus Integration
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D009707:Nucleosomes; D004247:DNA; D019427:HIV Integrase; C514801:p31 integrase protein, Human immunodeficiency virus 1