The Genome Recombination/Regulation Section focuses on two topics related to recombination and genome stability: mechanisms that generate DNA palindromic gene amplifications and the origin of DNA synthesis errors associated with genetic recombination. Studies on genome instability. We are continuing our analysis of how DNA palindromes are generated. These head to head DNA sequences are highly unstable. Some tumor cells undergo gene amplification by unknown mechanisms that generate palindromes. The instability of these sequences contributes to additional genome rearrangements that occur in tumors. Because palindromes are unstable in bacteria, it is it nearly impossible to clone them. Similarly, the secondary structures that can be adopted by palindromic DNAs make them very difficult to sequence. We opened the field of research on the origin of DNA palindromes by making progress in three important areas related to the study of palindromes. First, we identified yeast strains that tolerate palindromes. Second, we developed a method that allows us to sequence palindromic DNAs. Third, we developed a recombination substrate that generates palindromes and identified a class of recombinants that is almost exclusively palindromes. We demonstrated that the palindromes are formed in our system by a novel kind of nonhomologous end joining (NHEJ) which is independent of some of the recombination functions that are required for most NHEJ events. We recently demonstrated that we can isolate palindromic sequences from mammalian genomes, opening the door to the analysis of palindromes found in normal and malignant cells. We are collaborating on the analysis of DNA palindromes and inverted repeats found in human tumors. This common mechanism of gene amplification in tumors was not accessible to physical characterization until the breakthrough we made described above. We have developed new methods to isolate the novel junctions associated with DNA palindromes found in tumors. It is our expectation that the characterization of those junctions will help reveal details of the mechanism by which they are generated. Our similar approach to DNA palindromes in yeast was paradigm shifting in that it revealed a very different mechanism of formation quite unlike the generally accepted model.
