A Rous sarcoma virus provirus is flanked by short direct repeats of a cellular DNA sequence present in only one copy prior to integration.

The Rous sarcoma virus (RSV)-transformed rat cell line RSV-NRK-2 contains a single complete RSV provirus. We have obtained recombinant lambda clones that contain both ends of the RSV provirus and the flanking rat sequences. The provirus is integrated in unique DNA and is present in only one of the two homologous chromosomes. The rat sequences into which the RSV provirus integrated were also cloned from the RSV-NRK-2 cell line. The sequences of the regions involved in the recombination event have been determined and compared. Our data suggest that, compared with the sequence of viral DNA in the large circular form of unintegrated viral DNA, the provirus lacks two base pairs at each end and that the provirus is flanked by a six-base-pair direct repeat of cellular DNA. This six-base-pair repeat was apparently created during the integration event because this sequence was present only once at the integration site before the provirus was inserted. A survey of eight other independent RSV transformed rat cell lines demonstrates that, in agreement with earlier results, the RSV proviruses have entered different segments of rat cell DNA. We have also determined the sequence of a second virus DNA-host cell DNA junction from a second RSV-transformed rat cell line (RSV-NRK-4) and find that there are no obvious similarities between the two integration sites or between the integration sites and the termini of viral DNA.