title: PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity in Latvians, Lithuanians and Taiwanese.
abstract: 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.
authors.affiliation: Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Miera str. 3, LV2169, Salaspils, Latvia.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Sjakste
authors.affiliation: Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Miera str. 3, LV2169, Salaspils, Latvia.
authors.forename: Natalia
authors.initials: N
authors.lastname: Paramonova
authors.affiliation: Institute of Biomedicine, Tzu-Chi University, Tzu-Chi, Taiwan.
authors.forename: Lawrence Shi-Shin
authors.initials: LS
authors.lastname: Wu
authors.affiliation: Department of Laboratory Medicine, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
authors.forename: Zivile
authors.initials: Z
authors.lastname: Zemeckiene
authors.affiliation: Department of Pulmonology and Immunology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
authors.forename: Brigita
authors.initials: B
authors.lastname: Sitkauskiene
authors.affiliation: Department of Pulmonology and Immunology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
authors.forename: Raimundas
authors.initials: R
authors.lastname: Sakalauskas
authors.affiliation: Division of Allergy and Clinical Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Jiu-Yao
authors.initials: JY
authors.lastname: Wang
authors.affiliation: Faculty of Medicine, University of Latvia, Riga, Latvia ; Latvian Institute of Organic Synthesis, Riga, Latvia.
authors.forename: Nikolajs
authors.initials: N
authors.lastname: Sjakste
keywords: Genetic diversity; HWE, Hardy–Weinberg equilibrium; HapMap HCB, Han Chinese; HapMap JPT, Japanese; HapMap-CEU, NorthWestern Europeans; Human population; LD, linkage disequilibrium; LT, Lithuanian population; LV, Latvian population; PSMA3; PSMA6; PSMC6; Proteasome; SNP; SNP, single nucleotide polymorphism; T2DM, type 2 diabetes mellitus; TF, transcription factor; TFBS, transcription factor binding site; TW, Taiwanese population; UPS, ubiquitin–proteasome system