The G→C rs590352 in the Protein-Coding Region of ATXN7L3B Gene Upregulates Its Expression In Vivo

Previously using the omics data on allele-asymmetric gene expression (RNA-seq) and allele-asymmetry in the binding of regulatory proteins (ChIP-seq), we have determined rs590352 G→C as a potential regulatory polymorphism. Substitution G→C is situated in the protein-coding region of gene ATXN7L3B and is synonymic. The product of this gene competes with protein ATXN7L3 of the DUB module of transcription coactivator SAGA complex. The goal of our work is to study the effect of single nucleotide substitution G→C on the activity of putative cis-regulatory element in the exon 1 of ATXN7L3B. We use electrophoretic mobility shift assay (EMSA) to demonstrate that the G→C (rs590352) substitution damages the binding sites of certain transcription factors in the region of its localization. Dual luciferase assay demonstrates that this substitution significantly decreases the reporter gene expression when inserting the cassettes of double or triple repeats of the corresponding element upstream of heterologous promoter. The allele-asymmetric in vivo ATXN7L3B expression is lower in the case of allele C as compared with that of allele G. These data are useful for both the understanding of the regulation of poorly studied gene ATXN7L3B and a deeper insight into the functional role of SNPs in gene coding regions.