PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity in Latvians, Lithuanians and Taiwanese

6533b857fe1ef96bd12b44b1

RESEARCH PRODUCT

PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity in Latvians, Lithuanians and Taiwanese

Tatjana Sjakste Nikolajs Sjakste Lawrence Shi Shin Wu Raimundas Sakalauskas Zivile Zemeckiene Jiu Yao Wang Brigita Sitkauskiene Natalia Paramonova

subject

UPS ubiquitin–proteasome system Linkage disequilibrium TF transcription factor LD linkage disequilibrium Population SNP Locus (genetics)Single-nucleotide polymorphism Biology Article HapMap JPT Japanese Genetic diversity Human population TW Taiwanese population LT Lithuanian population Genetics International HapMap Project Allele education HapMap-CEU NorthWestern Europeans Genetics (clinical)Genetics education.field_of_study Genetic diversity Proteasome HapMap HCB Han Chinese HWE Hardy–Weinberg equilibrium Haplotype PSMC6 LV Latvian population T2DM type 2 diabetes mellitus PSMA6 SNP single nucleotide polymorphism TFBS transcription factor binding site PSMA3

description

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; r2 = 1) and slightly disrupted in Taiwanese (D´ = 0.978; r2 = 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.

year	journal	country	edition	language
2014-12-01	Meta Gene

https://doi.org/10.1016/j.mgene.2014.03.002