Conservation and evolution of (CT) n/(GA) n microsatellite sequences at orthologous positions in diverse mammalian genomes

Abstract

The distribution and evolution of (CT) n microsatellites were examined in GenBank mammalian DNA sequences because these microsatellites are known to play important roles in the regulation of some genes in Drosophila melanogaster. A total of 236 (CT) n micro-satellite loci were found in GenBank mammalian gene sequences. To determine whether (CT) n microsatellite arrays were conserved at orthologous positions in distantly related mammalian sequences, we determined whether orthologous sequences existed in GenBank for each of the 236 loci. A total of 47 sequence alignments could be made. For rodent X rodent comparisons, 7 of 8 (CT) n arrays were conserved at identical positions in each pair of orthologous sequences. Comparisons of orthologous sequences between different orders of mammals indicated that 11 of 39 (CT) n arrays occurred at orthologous positions or within 1 kb of orthologous positions in each pair of sequences. It appears that there is some level of conservation of (CT) n repeats in distantly related mammals. However, this level of conservation may not be greater than what might be expected to occur by chance. In 13 cases where (CT) n arrays were not conserved at orthologous positions, the lack of a (CT) n array in one sequence resulted from either nucleotide substitution within an array or nonexpansion of a shorter (CT) n element. In these cases, significant sequence identity could be detected throughout the entire region even though the repeat array was not detected in one of the sequences. In contrast, there was a disruption of sequence identity in the (CT) n microsatellite region that ranged from 24 to 1600 bp in 21 cases. In some cases, the disruption in homology occurred on only the immediate 3′ or 5′ side of the repeat array. The disruption of sequence identity occurred even in some instances in which the array was conserved. Insertion of human Alu or mouse B1 elements was responsible for the disruption of homology in three cases. In the majority of cases, the disruption in homology resulted from insertion or deletion of nonrepetitive DNA. The possible role of (CT) n arrays in evolutionary processes is discussed.