Determination of allelic expression of SNP rs1880676 in choline acetyltransferase gene in HeLa cells

• Choline acetyltransferase (ChAT) influences a wide range of brain functions.
• Variants in ChAT are associated with nicotine dependence (ND).
• SNP rs1880676 is a non-synonymous variant located in the code region of ChAT.
• The G allele of rs1880676 is expressed significantly higher than A allele at RNA and protein levels.
• SNP rs1880676 is functional variant that plays a significant role in developing ND.

Recently, we reported that several polymorphisms and haplotypes in the choline acetyltransferase gene (ChAT) are associated with nicotine dependence (ND). Of them, SNP rs1880676 is of particular interest because: (1) it is a non-synonymous variant located in the coding region of an alternatively spliced form of ChAT and (2) it is located in several haplotypes that are significantly associated with ND. The objective of this study was to determine, using an in vitro system, whether the alleles G (coding for aspartic acid) or A (coding for asparagine) of rs1880676 have any allele-specific effect on ChAT expression. We first used site-directed mutagenesis to construct two expression vectors differed in the allelic position of rs1880676 (G/A), which were transfected into HeLa cells. We then measured expression of ChAT associated with each allele. We found significant expression differences for the two alleles, with the G allele being expressed significantly greater than A allele (P < 0.01 at both mRNA and protein levels). Further, we validated the ChAT expression of the G allele was significantly higher than that of the A allele by using ELISA assay (P = 0.00016). We concluded that rs1880676 is functional and that the allelic variations of this polymorphism are involved in developing ND by altering ChAT expression.