Long terminal repeat (LTR)-derived recombination of retroviral DNA: sequence analyses of an aberrant clone of baboon endogenous virus DNA which carries an inversion from the LTR to the gag region.

Nucleotide sequences of a cloned proviral DNA of baboon endogenous virus M7 were analyzed, which carried an internal inversion. The inversion of 2.2 kilobase pairs was occurred between the junction of two tandem LTRs and a site locating in the p30 region of the gag gene. The ATAA sequence was a target for recombination generating the inversion, which was duplicated at both ends of the inverted segment. AAA and CA were lost at the 5'- and 3'-ends of the LTRs by the inversion, respectively. On both sides of the target sequence, long AG-rich stretches were detected, which may specify the site of recombination together with the target sequence. The characteristic base changes in the inversion are concluded to result from an illegitimate recombination associated with LTRs, as well as in case of provirus integration into the host cell DNA. We propose and discuss models to explain the processes of recombination to generate both inversion and integration.