Sjakste Tatjana, Paramonova Natalia, Wu Lawrence Shi-Shin, Zemeckiene Zivile, Sitkauskiene Brigita, Sakalauskas Raimundas, Wang Jiu-Yao, Sjakste Nikolajs
Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Miera str. 3, LV2169, Salaspils, Latvia.
Institute of Biomedicine, Tzu-Chi University, Tzu-Chi, Taiwan.
Meta Gene. 2014 Apr 17;2:283-98. doi: 10.1016/j.mgene.2014.03.002. eCollection 2014 Dec.
PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity was investigated in 1438 unrelated subjects from Latvia, Lithuania and Taiwan. In general, polymorphism of each individual locus showed tendencies similar to determined previously in HapMap populations. Main differences concern Taiwanese and include presence of rs2277460 rare allele A not found before in Asians and absence of rs2295827 rare alleles homozygotes TT observed in all other human populations. Observed patterns of SNPs and haplotype diversity were compatible with expectation of neutral model of evolution. Linkage disequilibrium between the rs2295826 and rs2295827 was detected to be complete in Latvians and Lithuanians (D´ = 1; r(2) = 1) and slightly disrupted in Taiwanese (D´ = 0.978; r(2) = 0.901). Population differentiation (FST statistics) was estimated from pairwise population comparisons of loci variability, five locus haplotypes and PSMA6 and PSMC6 two locus haplotypes. Latvians were significantly different from all Asians at each of 5 SNPs and from Lithuanians at the rs1048990 and PSMC6 loci. Lithuanian and Asian populations exhibited similarities at the PSMC6 loci and were different at the PSMA6 and PSMA3 SNPs. Considering five locus haplotypes all European populations were significantly different from Asian; Lithuanian population was different from both Latvian and CEU. Allele specific patterns of transcription factor binding sites and splicing signals were predicted in silico and addressed to eventual functionality of nucleotide substitutions and their potential to be involved in human genome evolution and geographical adaptation. Current study represents a novel step toward a systematic analysis of the proteasomal gene genetic diversity in human populations.
在来自拉脱维亚、立陶宛和台湾的1438名无亲缘关系的个体中，对PSMA6（rs2277460、rs1048990）、PSMC6（rs2295826、rs2295827）和PSMA3（rs2348071）的基因多样性进行了研究。总体而言，每个个体位点的多态性表现出与先前在HapMap群体中确定的趋势相似。主要差异涉及台湾人群，包括亚洲人之前未发现的rs2277460稀有等位基因A的存在，以及在所有其他人群中观察到的rs2295827稀有等位基因纯合子TT的缺失。观察到的单核苷酸多态性（SNP）和单倍型多样性模式与中性进化模型的预期相符。在拉脱维亚人和立陶宛人中，检测到rs2295826和rs2295827之间的连锁不平衡是完全的（D´ = 1；r² = 1），而在台湾人群中略有破坏（D´ = 0.978；r² = 0.901）。通过对位点变异性、五个位点单倍型以及PSMA6和PSMC6两个位点单倍型的成对群体比较，估计了群体分化（FST统计量）。在5个单核苷酸多态性位点上，拉脱维亚人与所有亚洲人显著不同，在rs1048990和PSMC6位点上与立陶宛人显著不同。立陶宛人群体和亚洲人群体在PSMC6位点上表现出相似性，而在PSMA6和PSMA3单核苷酸多态性位点上存在差异。考虑五个位点的单倍型，所有欧洲人群体与亚洲人群体都有显著差异；立陶宛人群体与拉脱维亚人群体和CEU群体都不同。通过计算机模拟预测了转录因子结合位点和剪接信号的等位基因特异性模式，并探讨了核苷酸替代的最终功能及其参与人类基因组进化和地理适应性的潜力。当前的研究代表了朝着系统分析人类群体中蛋白酶体基因遗传多样性迈出的新一步。
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