Nucleotide sequence analysis of novel junctions near an unstable integrated plasmid in human cells

Characterization of human cell clones containing a promoterless selectable gene (neo), integrated at various locations in the genome, demonstrated that one of the integration sites had a high rate of spontaneous tandem duplications. Other investigators have suggested that specific sequences, such as short repeats, found near an integration site, could be responsible for this kind of instability. To learn more about this process, we sequenced the DNA at the recombination site in two independently derived subclones, and compared these sequences with those found in the parental cell DNA. The results demonstrate that specific sequences are not required at the recombination site. In one G418-resistant subclone, recombination occurred between an Alu retroposon in the cellular DNA and integrated pBR322 sequences sharing 3 bp of similarity at the recombination site. In the other subclone, recombination occurred between single-copy cellular DNA and integrated simian virus 40 sequences sharing a single bp of similarity at the recombination site. This heterogeneity at the recombination site indicates a general enhancement of the rate of recombination within the entire region, with little if any sequence specificity or similarity required.