Yandava C N, Gastier J M, Pulido J C, Brody T, Sheffield V, Murray J, Buetow K, Duyk G M
Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Genome Res. 1997 Jul;7(7):716-24. doi: 10.1101/gr.7.7.716.
The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from approximately 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.
作为推进我们对微卫星重复序列进化理解的第一步，对Alu重复元件亚类与各类三核苷酸和四核苷酸微卫星的关联进行了表征。此外，关于特定类微卫星与Alu元件家族关联的信息被用于促进遗传标记的开发。由于无法设计独特的引物，含有Alu重复序列的序列被剔除。各类微卫星与不同类别的Alu重复序列相关联。非常丰富且富含多聚腺苷酸的微卫星类别（ATA、AATA）经常与进化上较古老的Alu重复亚类AluSx相关联，而大多数GATA和CA微卫星与最近的Alu亚家族AluY相关联。我们的观察结果支持Alu重复序列与微卫星关联的所有三种可能机制。使用来自特定微卫星类别的一组序列设计的引物与该类别的更多序列具有更高的同源性，比为其他类别设计的探针更高。我们开发了一种高效的方法，用本研究设计的探针预筛选GGAA和ATA微卫星克隆中的Alu重复序列。我们还表明，在单一反应中标记的Alu探针（多重标记）可有效地用于GGAA克隆的预筛选。对这些预筛选的GGAA微卫星进行测序发现只有5%的Alu重复序列。用为ATA微卫星类别设计的引物进行预筛选，使标记的损失从大约50%减少到10%。设计的新Alu探针也已证明在Alu-Alu指纹图谱分析中有用。
