Discovery of functional non-coding conserved regions in the α-synuclein gene locus

Abstract

Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the α-synuclein (SNCA) gene have consistently been shown to be associated with Parkinson’s disease, but the functional relevance is unclear. Based on these findings we hypothesized that conserved cis-regulatory elements in theSNCAgenomic region regulate expression ofSNCA, and that SNPs in these regions could be functionally modulating the expression ofSNCA, thus contributing to neuronal demise and predisposing to Parkinson’s disease.In a pair-wise comparison of a 206kb genomic region encompassing theSNCAgene, we revealed 34 evolutionary conserved DNA sequences between human and mouse. All elements were cloned into reporter vectors and assessed for expression modulation in dual luciferase reporter assays.  We found that 12 out of 34 elements exhibited either an enhancement or reduction of the expression of the reporter gene. Three elements upstream of theSNCAgene displayed an approximately 1.5 fold (p<0.009) increase in expression. Of the intronic regions, three showed a 1.5 fold increase and two others indicated a 2 and 2.5 fold increase in expression (p<0.002). Three elements downstream of theSNCAgene showed 1.5 fold and 2.5 fold increase (p<0.0009). One element downstream ofSNCAhad a reduced expression of the reporter gene of 0.35 fold (p<0.0009) of normal activity.Our results demonstrate that theSNCAgene contains cis-regulatory regions that might regulate the transcription and expression ofSNCA. Further studies in disease-relevant tissue types will be important to understand the functional impact of regulatory regions and specific Parkinson’s disease-associated SNPs and its function in the disease process.