Clustered illegitimate recombination events in mammalian cells involving very short sequence homologies

Mammalian cells possess mechanisms that allow unrelated sequences to recombine (illegitimate recombination), This is evidenced by the high rate of recombination between largely non-homologous sequences after DNA transfection1,2. We have analysed the integrated viral sequences present in the polyoma transformed cell line 82-Rat3. Within the single insert of integrated viral sequences there are two regions where multiple recombination events have occurred. The recombination events are particularly interesting as there was no obvious prior selection for their occurrence, and thus they may accurately reflect a normal mechanism of cellular recombination. A total of five recombinant joins have been sequenced. Our results, reported here, indicate that multiple recombinant events occur within small regions (about 50 bp) and that very short homologous stretches (3–4 bp) participate in joining two non-homologous sequences. This suggests that factors other than sequence homologies drive certain recombination events. These results have implications for site-directed recombination following the addition of exogenous DNA.