Nucleotide sequence variation, homogenization, and evolution of X chromosome alpha satellite DNA

A substantial portion of the DNA of eukaryotic genomes is organized as tandemly repeated sequences, generally referred to as satellite DNA. A number of evolutionary processes, such as sequence conversion, unequal crossing over, and molecular drive have been postulated to maintain the homogeneity of tandemly repeated DNA arrays. Insightful characterization of the degree of sequence homogeneity in satellite DNA families has been limited by the lack of information about the organization of the repeat sequences of many satellite families. In humans, the chromosome-specific higher-order repeat organization of alpha satellite, a centromerically located DNA family, has been extensively characterized, providing a framework within which to more fully investigate the relative contribution and extent of genomic turnover processes. To this end, a systematic approach of analysis of the degree of sequence divergence within alpha satellite arrays from the same X chromosome and between arrays from the same and different X chromosomes was performed. The observed patterns of nucleotide sequence variation implicated effectively short-range mechanisms in the maintenance of sequence homogeneity of the arrays. A description of within population sequence variation provides the basis for comparisons of sequence variation between populations or between species.;The characteristic high degree of sequence homogeneity of satellite DNA repeats within populations is contrasted with the variability noted when nucleotide sequences of the same satellite DNA repeat family from different species are compared, a pattern called concerted evolution. To elucidate events in the organization of alpha satellite higher-order repeats on the X chromosome, the organization of gorilla alpha satellite sequences homologous to the human X chromosome were investigated. The description of an ancestral sequence common to both species' repeats provides insight into events in the evolution of X chromosome alpha satellite DNA, and by extension, in other tandemly repeated multicopy DNA families.