Microsatellites and other simple sequences: genomic context and mutational mechanisms

<jats:title>Abstract</jats:title> <jats:p>'Microsatellite' is now the commonest term used to describe tandem repeats of short sequence motifs (no more than six bases long). Microsatellites have been found in every organism investigated so far. They may be highly polymorphic, especially if long and uninterrupted, and they are therefore useful genetic markers. Microsatellite-like sequences made up of concentrations of specific motifs that are not tandemly repeated are known as cryptically simple, and such sequences are also widespread, although generally more common in organisms with large genomes. The functional significance of such sequences is still unknown although they are sometimes found within exons and have been associated with diseases. Microsatellites appear to be more or less uniformly distributed across eukaryotic genomes, but are under-represented in coding regions, and perhaps telomeres. Repeats of poly(A)/poly(T) are the most common microsatellites in all genomes, but beyond that different genomes show subtly different frequency distributions. Genetic and other studies suggest that slipped-strand mispairing during replication is the predominant mechanism of mutation of microsatellites, but recently an increasing amount of circumstantial evidence has also implicated recombination.</jats:p>