Mutation Biases and Mutation Rate Variation Around Very Short Human Microsatellites Revealed by Human–Chimpanzee–Orangutan Genomic Sequence Alignments

I have studied mutation patterns around very short microsatellites, focusing mainly on sequences carrying only two repeat units. By using human–chimpanzee–orangutan alignments, inferences can be made about both the relative rates of mutations and which bases have mutated. I find remarkable non-randomness, with mutation rate depending on a base’s position relative to the microsatellite, the identity of the base itself and the motif in the microsatellite. Comparing the patterns around (AC)2 with those around other four-base combinations reveals that (AC)2 does not stand out as being special in the sense that non-repetitive tetramers also generate strong mutation biases. However, comparing (AC)2 and (AC)3 with (AC)4 reveals a step change in both the rate and nature of mutations occurring, suggesting a transition state, (AC)4 exhibiting an alternating high–low mutation rate pattern consistent with the sequence patterning seen around longer microsatellites. Surprisingly, most changes in repeat number occur through base substitutions rather than slippage, and the relative probability of gaining versus losing a repeat in this way varies greatly with repeat number. Slippage mutations reveal rather similar patterns of mutability compared with point mutations, being rare at two repeats where most cause the loss of a repeat, with both mutation rate and the proportion of expansion mutations increasing up to 6–8 repeats. Inferences about longer repeat tracts are hampered by uncertainties about the proportion of multi-species alignments that fail due to multi-repeat mutations and other rearrangements.