Evolution of tandemly repeated DNA: Repeat unit variation of human alpha satellite DNA.

摘要

Alpha satellite DNA, a family of tandemly repeated DNA found at the centromeres of all human and primate chromosomes examined, has a high degree of homogeneity between repeat units within species and chromosomes. Insight into the complex interplay of the genetic mechanisms that lead to this concerted evolution, such as mutation, unequal crossing-over, and inter- and intrachromosomal recombination, can be gained by examination of the patterns of variation of alpha satellite DNA within species, populations, and chromosomes.;PCR amplified alpha satellite DNA allows the simultaneous analysis of multiple repeat units, where sequence variation is revealed as two bands at the same position on a sequencing ladder. Such analysis of alpha satellite from several chromosomes 17 detected extensive haplotype-specific sequence variation, not simply the presence or absence of rare mutations. Subsequent phylogenetic analysis of sequence variation in multiple independent cloned repeat units showed that chromosome 17 alpha satellite repeat units evolve primarily along haplotypic lineages. Thus, the homogenization of repeat units on individual homologues (along haploid lineages) is relatively more efficient than between homologous chromosomes.;The human chromosome 17-specific subset of alpha satellite is characterized by several polymorphic repeat units of different length. These repeat units were found by two-dimensional DNA electrophoresis to be localized into large homogeneous domains of up to several hundred kilobase pairs, instead of being interspersed throughout the megabased size arrays, suggesting that genetic exchanges such as unequal crossing-over occur primarily between sister chromatids misaligned by one or few repeat units. PCR amplification of chromosome-specific alpha satellite revealed polymorphic repeat units, and could be used for haplotypic analysis of chromosome 17. The putative unequal crossing-over events that give rise to a set of 13 variant repeat units were found to cluster within a distinct region of 20-25 bp within the consensus repeat unit, as opposed to occurring randomly, perhaps due to secondary characteristics such as chromatin structure. Furthermore, recognition sites for the alpha satellite binding protein CENP-B were found to be juxtaposed in each misalignment of repeat units, suggesting a possible role for this protein in these recombination events.