ANALYSIS OF AGE-ASSOCIATED MITOCHONDRIAL-DNA DELETION BREAKPOINT REGIONS FROM MICE SUGGESTS A NOVEL MODEL OF DELETION FORMATION

Mitochondrial genomes with multiple types of DNA deletions have been s hown to accumulate with age in various tissues from humans, monkeys, r ats, mice, and C. elegans. The deleted genomes have been classified ba sed on characteristics of the deletion breakpoints such as the presenc e (or absence) of direct repeat sequences. The prevalence of direct re peats located precisely at deletion breakpoints in human mitochondrial DNA deleted genomes has led several investigators to propose slip rep lication or recombination as mechanisms of deletion formation. Other s equence motifs such as topoisomerase II cleavage recognition sites and secondary or tertiary structures have also been implicated in aiding deletion formation. We have characterized, from mouse skeletal muscle and brain tissues, the breakpoint regions from 36 mitochondrial genome s with deletions. Based on the large number of deletion breakpoints pr ecisely flanked by small (2-4 nucleotides) direct repeats, we propose ''replication jumping'' as an important mechanism of deletion formatio n, In this model, the polymerase stutters during replication, possibly in an area that has been oxidatively modified. The nascent strand the n anneals to a complementary downstream region and replication continu es after the removal of any single-stranded ''excess'' DNA up to a dou ble-stranded region, resulting in a mutant genome.