Monitoring mammalian genome rearrangement with mid-repetitive sequences as probes

By utilization of mid-repetitive sequences, the intracisternal A particle (IAP) gene, as a probe, genome rearrangement involving IAP genes and their neighboring sequences in rodent cells can be monitored. This is based on electrophoretic separation of the twice digested restriction fragments of genomic DNA in a 2-D pattern. The first digestion was done in solution followed by electrophoresis of the restriction fragments in the first dimension. A second restriction enzyme digestion was carried out in situ in the gel followed by electrophoresis in a second dimension perpendicular to the first electrophoresis. After Southern blotting, the DNA on the filter is hybridized with a probe that is a fragment located near the 5' end of the IAP gene, but does not overlap with the 5' long terminal repeat (LTR). The exposed X-ray film revealed about 370 distinct spots in the 2-D maps. In comparing the 2-D maps, genome rearrangement involving IAP was detected.