Grimaldi M C, Crouau-Roy B
Centre d'Immunopathologie et de Génétique Humaine, CNRS, UPR 8291, CHU Purpan, Toulouse, France.
J Mol Evol. 1997 Mar;44(3):336-40. doi: 10.1007/pl00006151.
Microsatellite DNA sequences have become the dominant source of nuclear genetic markers for most applications. It is important to investigate the basis of variation between alleles and to know if current assumptions about the mechanisms of microsatellite mutation (that is to say, variations involving simple changes in the number of repeat) are correct. We have characterized, by DNA sequencing, the human alleles of a new highly informative (CA)n repeat localized approximately 20 kb centromeric to the HLA-B gene. Although 12 alleles were identified based on conventional length criteria, sequencing of the alleles demonstrated that differences between alleles were found to be more complex than previously assumed: A high degree of microsatellite variability is due to variation in the region immediately flanking the repeat. These data indicate that the mutational process which generates polymorphism in this region has involved not only simple changes in the number of dinucleotide CA repeats but also perturbations in the nonrepeated 5' and 3' flanking sequences. Three families of alleles (not visible from the overall length of the alleles), with presumably separate evolutionary histories, exist and can yield to homoplasy of size. Effectively, we can observe alleles of the same size with different internal structures which are separated by a significant amount of variation. Although allelic homoplasy for non-interrupted microsatellite loci has been suggested between different species, it has not been unequivocally demonstrated within species. A strong association is noted between alleles defined at the sequence level and HLA-B alleles. The observation of several families of alleles at the population level provides information about the evolutionary history and mutation processes of microsatellites and may have implications for the use of these markers in phylogenetic, linkage disequilibrium studies, and gene mapping.
微卫星DNA序列已成为大多数应用中核基因标记的主要来源。研究等位基因间变异的基础，并了解当前关于微卫星突变机制（即涉及重复序列数量简单变化的变异）的假设是否正确，这一点很重要。我们通过DNA测序，对一个新的高信息性（CA）n重复序列的人类等位基因进行了特征分析，该重复序列位于HLA - B基因着丝粒方向约20 kb处。尽管根据传统长度标准鉴定出了12个等位基因，但对等位基因的测序表明，等位基因之间的差异比之前假设的更为复杂：高度的微卫星变异性是由于紧邻重复序列区域的变异所致。这些数据表明，在该区域产生多态性的突变过程不仅涉及二核苷酸CA重复序列数量的简单变化，还包括非重复的5'和3'侧翼序列的扰动。存在三个等位基因家族（从等位基因的整体长度上不可见），它们可能具有独立的进化历史，并且会导致大小的同塑性。实际上，我们可以观察到大小相同但内部结构不同的等位基因，它们之间存在大量变异。虽然在不同物种之间已有人提出非中断微卫星位点存在等位基因同塑性，但在物种内部尚未得到明确证实。在序列水平定义的等位基因与HLA - B等位基因之间存在强烈关联。在群体水平上对等位基因家族的观察为微卫星的进化历史和突变过程提供了信息，并且可能对这些标记在系统发育、连锁不平衡研究和基因定位中的应用产生影响。
