Genetic instabilities of (CCTG)-(CAGG) and (ATTCT)-(AGAAT) disease-associated repeats reveal multiple pathways for repeat deletion

The DNA repeats (CTG)-(CAG), (CGG)-(CCG), (GAA)-(TTC), (ATTCT)-(AGAAT), and (CCTG)-(CAGG), undergo expansion in humans leading to neurodegenerative disease. A genetic assay for repeat instability has revealed that the activities of RecA and RecB during replication restart are involved in a high rate of deletion of (CTG)-(CAG) repeats in E. coli. This assay has been applied to (CCTG)-(CAGG) repeats associated with myotonic dystrophy type 2 (DM2) that expand to 11 000 copies and to spinocerebellar ataxia type 10 (SCA10) (ATTCT)-(AGAAT) repeats that expand to 4500 copies in affected individuals. DM2 (CCTG)-(CAGG) repeats show a moderate rate of instability, less than that observed for the myotonic dystrophy type 1 (CTG)-(CAG) repeats, while the SCA10 (ATTCT)-(AGAAT) repeats were remarkably stable in E. coli. In contrast to (CTG)(CAG) repeats, deletions of the DM2 and SCA10 repeats were not dependent on RecA and RecB, suggesting that replication restart may not be a predominant mechanism by which these repeats undergo deletion. These results suggest that different molecular mechanisms, or pathways, are responsible for the instability of different disease-associated DNA repeats in E. coli. These pathways involve simple replication slippage and various sister strand exchange events leading to deletions or expansions, often associated with plasmid dimerization. The differences in the mechanisms of repeat deletion may result from the differential propensity of these repeats to form various DNA secondary structures and their differential proclivity for primer-template misalignment during replication.