Structural Aspects of Homologous DNA-DNA Interactions Revealed by Partitioning of RIP Mutations

In some fungi, a process known as Repeat-Induced Point mutation (RIP) can accurately identify and mutate nearly all genesized DNA repeats present in the haploid premeiotic nuclei. Studies of RIP in Neurospora crassa have suggested that the sequence homology is detected between intact double helices without strand separation and participation of RecA homologs. These studies relied on the aggregated number of mutations as a simple quantitative readout of RIP activity and did not try interpret the distributions of mutations along DNA. Important additional information can be extracted by transforming these distributions into profiles of a new parameter called partitioned RIP propensity (PRP) which takes into account the site density as well as the sequence context. This approach revealed surprising systematic variations of PRP due to the position of a given DNA segment relative to the homology boundaries and its topology. Notably, identical pairs of direct versus inverted repeats produce very distinct PRP profiles. This effect could be rationalized assuming a specific redistribution of the supercoiling stress produced by the previously discovered untwisting of paired of DNA homologs. Similar mechanisms account for other persistent features of PRP profiles, and this general topological model raises an intriguing possibility that local DNA supercoiling provoked by homologous dsDNA-dsDNA pairing can modulate the overall structure and properties of repetitive DNA. These effects can be particularly strong in the context of long tandem repeat arrays that are typically present at the (peri)centromeric regions of chromosomes.