Unequal cross-over is involved in human alpha satellite DNA rearrangements on a border of the satellite domain.

It can be invoked from the theory of tandem repeat homogenization that DNA on a satellite/non-satellite border may carry sequence marks of molecular processes basic to satellite evolution. We have sequenced a continuous 17-kb alpha satellite fragment bordering the non-satellite in human chromosome 21, which is devoid of higher-order repeated structure, contains multiple rearrangements, and exhibits higher divergence of monomers towards the border, indicating the lack of efficient homogenization. Remarkably, monomers have been found with mutually supplementary deletions matching each other as reciprocal products of unequal recombination, which provide evidence for unequal cross-over as a mechanism generating deletions in satellite DNA.