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Nucleic Acids Research, 2001, Vol. 29, No. 18 3814-3821
© 2001 Oxford University Press

The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination

Abdeladim Moumen, Lucette Polomack, Bernard Roques2, Henri Buc1 and Matteo Negroni*

Unité de Régulation Enzymatique des Activités Cellulaires, FRE 2364-CNRS, Département de Biologie Moléculaire and 1URA 1960-CNRS, Institut Pasteur, 25–28 rue du Docteur Roux, 75724 Paris cedex 15, France and 2Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, 4 avenue de l’Observatoire, 75270 Paris cedex 06, France

Template switching during reverse transcription is crucial for retroviral replication. While strand transfer on the terminal repeated sequence R is essential to achieve reverse transcription, template switching from internal regions of the genome (copy choice) leads to genetic recombination. We have developed an experimental system to study copy-choice recombination in vitro along the HIV-1 genome. We identify here several genomic regions, including the R sequence, where copy choice occurred at high rates. The frequency of copy choice occurring in a given region of template was strongly influenced by the surrounding sequences, an observation that suggests a pivotal role of the folding of template RNA in the process. The sequence R, instead, constituted an exception to this rule since it was a strong hot-spot for copy choice in the different sequence contexts tested. We suggest therefore that the structure of this region has been optimised during viral evolution to ensure efficient template switching independently from the sequences that might surround it.

* To whom correspondence should be addressed. Tel: +33 1 4568 8505; Fax: +33 1 4568 8399; Email: matteo{at}pasteur.fr


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