Identification of a deletion hotspot on distal mouse chromosome 4 by YAC fingerprinting

Using repetitive elements as probes, genomic DNA fingerprints of four rando mly selected yeast artificial chromosome (YAC) clones (two human and two mo use-derived YAC) were analyzed to determine the mutation level following X- ray exposure. Because the repetitive probes were derived from the mammalian host DNA, most of the fingerprint bands originated from the artificial chr omosomes and not from the yeast genome. For none of the YAC clones was the mutation frequency elevated following X-ray exposure. However, for one mous e-derived YAC, the mutation level was unusually high (7%; 42 mutants of 607 clones analyzed), whereas for the other three YACs, the mutation level was nearly 0%. Surprisingly, 40 of the 42 mutations were deletions occurring o nly at three of the 20 mouse specific fingerprint bands. One of the frequen tly deleted fragments was cloned, sequenced and mapped to distal mouse chro mosome 4, which has been repeatedly reported to be the most unstable region of the whole mouse genome, associated with various tumors. Deletion mappin g of six YAC mutants revealed this fragment to be completely deleted in fou r YACs. In the other two mutants, recombination occurred within the fragmen t, in each case initiated at the same LINE-1 element. In conclusion, the pr esented YAC fingerprint is a useful tool for detecting and characterizing u nstable regions in mammalian genomes. (C) 2001 Elsevier Science B.V. All ri ghts reserved.