Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression
Author(s)Soldner, Frank; Stelzer, Yonatan; Abraham, Brian J.; Latourelle, Jeanne C.; Barrasa, M. Inmaculada; Goldmann, Johanna; Myers, Richard H.; Young, Richard A; Jaenisch, Rudolf; Shivalila, Chikdu Shakti; ... Show more Show less
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Genome-wide association studies (GWAS) have identified numerous genetic variants associated with complex diseases, but mechanistic insights are impeded by a lack of understanding of how specific risk variants functionally contribute to the underlying pathogenesis. It has been proposed that cis-acting effects of non-coding risk variants on gene expression are a major factor for phenotypic variation of complex traits and disease susceptibility. Recent genome-scale epigenetic studies have highlighted the enrichment of GWAS-identified variants in regulatory DNA elements of disease-relevant cell types. Furthermore, single nucleotide polymorphism (SNP)-specific changes in transcription factor binding are correlated with heritable alterations in chromatin state and considered a major mediator of sequence-dependent regulation of gene expression. Here we describe a novel strategy to functionally dissect the cis-acting effect of genetic risk variants in regulatory elements on gene expression by combining genome-wide epigenetic information with clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9 genome editing in human pluripotent stem cells. By generating a genetically precisely controlled experimental system, we identify a common Parkinson’s disease associated risk variant in a non-coding distal enhancer element that regulates the expression of α-synuclein (SNCA), a key gene implicated in the pathogenesis of Parkinson’s disease. Our data suggest that the transcriptional deregulation of SNCA is associated with sequence-dependent binding of the brain-specific transcription factors EMX2 and NKX6-1. This work establishes an experimental paradigm to functionally connect genetic variation with disease-relevant phenotypes.
DepartmentMassachusetts Institute of Technology. Department of Biology
Nature Publishing Group
Soldner, Frank et al. “Parkinson-Associated Risk Variant in Distal Enhancer of α-Synuclein Modulates Target Gene Expression.” Nature 533.7601 (2016): 95–99.
Author's final manuscript