Structural analysis of a carcinogen-induced genomic rearrangement event.
We have explored the mechanism of genomic rearrangement in a hamster fibroblast cell culture system in which rearrangements are induced 5' to the endogenous thymidine kinase gene by chemical carcinogen treatment. The wild-type region around one rearrangement breakpoint was cloned and sequenced. With this sequence information, the carcinogen-induced rearrangement was cloned from the corresponding rearranged cell line by the inverse polymerase chain reaction. After the breakpoint fragment was sequenced, the wild-type rearrangement partner (RP15) was isolated by a second inverse polymerase chain reaction of unrearranged DNA. Comparison of the sequence of the rearrangement breakpoint with the wild-type RP15 and 5' thymidine kinase gene regions revealed short repeats directly at the breakpoint, as well as nearby A + T-rich regions in each rearrangement partner. Pulsed-field electrophoresis analysis demonstrated that this rearrangement is an interstitial deletion of 35 kilobases. Southern blot analysis of the RP15 region in unrearranged parental cells showed a demethylated CpG island and a complex of DNase I-hypersensitive sites adjacent to the breakpoint in the region deleted by the rearrangement. Therefore, these studies reveal interesting sequence and chromatin features near the rearrangement breakpoints and suggest a role for nuclear organization in the mechanism of carcinogen-induced genomic rearrangement.
Barr
F G
FG
Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, PA 19104.
Davis
R J
RJ
Eichenfield
L
L
Emanuel
B S
BS
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002273:Carcinogens / Q000494:pharmacology*; D002460:Cell Line; D002843:Chromatin / Q000648:ultrastructure; D006224:Cricetinae; D003412:Cricetulus; D015321:Gene Rearrangement; D008745:Methylation; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D015183:Restriction Mapping; D013937:Thymidine Kinase / Q000235:genetics*
D002273:Carcinogens; D002843:Chromatin; D013937:Thymidine Kinase