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

Template switching during reverse transcription is crucial for retroviral r eplication. While strand transfer on the terminal repeated sequence R is es sential 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 vit ro along the HIV-1 genome. We identify here several genomic regions, includ ing the R sequence, where copy choice occurred at high rates. The frequency of copy choice occurring in a given region of template was strongly influe nced by the surrounding sequences, an observation that suggests a pivotal r ole 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 c opy 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 th at might surround it.