RECOMBINATION IN THE 5'-LEADER OF MURINE LEUKEMIA-VIRUS IS ACCURATE AND INFLUENCED BY SEQUENCE IDENTITY WITH A STRONG BIAS TOWARD THE KISSING-LOOP DIMERIZATION REGION

Retroviral recombination occurs frequently during reverse transcriptio n of the dimeric RNA genome. By a forced recombination approach based on the transduction of Akv murine leukemia virus vectors harboring a p rimer binding site knockout mutation and the entire 5' untranslated re gion, we studied recombination between two closely related naturally o ccurring retroviral sequences. On the basis of 24 independent template switching events within a 481-nucleotide target sequence containing m ultiple sequence identity windows, we found that shifting from vector RNA to an endogenous retroviral RNA template during minus-strand DNA s ynthesis occurred within defined areas of the genome and did not lead to misincorporations at the crossover site. The nonrandom distribution of recombination sites did not reflect a bias for specific sites due to selection at the level of marker gene expression. We address whethe r template snitching is affected by the length of sequence identity, b y palindromic sequences, and/or by putative stem-loop structures. Sixt een of 24 sites of recombination colocalized with the kissing-loop dim erization region, and we propose that RNA-RNA interactions between pal indromic sequences facilitate template switching. We discuss the putat ive role of the dimerization domain in the overall structure of the re verse-transcribed RNA dimer and note that related mechanisms of templa te switching may be found in remote RNA viruses.