An algorithmic analysis of the role of unequal crossover in alpha-satellite DNA evolution

Human DNA consists of a large number of tandem repeat sequences. Such sequences are usually called satellites, with the primary example being the centromeric alpha-satellite DNA. The basic repeat unit of the alpha-satellite DNA is a 171 bp monomer. However, with the exception of peripheral alpha-satellite DNA, monomers can be grouped into blocks of k-monomers (4 < k < 20) between which the divergence rate is much smaller (e.g. 5%). Perhaps the simplest and best understood mechanism for tandem repeat array evolution is the unequal crossover. Although it is possible that the alpha-satellite sequence developed as a result of subsequent unequal crossovers only, no formal computational framework seems to have been developed to verify this possibility. In this paper we develop such a framework and perform experiments which seem to indicate that pericentromeric alpha-satellite segments (which are devoid of higher-order structure) are evolutionarily distinct from the higher-order repeat segments. It is likely that the higher order repeats developed independently in distinct regions of the genome and were carried into their current locations through an unknown mechanism of transposition.