Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression.
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.
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Frank
F
Soldner
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Yonatan
Y
Stelzer
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.|Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, Massachusetts 02139, USA.
Chikdu S
CS
Shivalila
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Brian J
BJ
Abraham
Department of Neurology, Boston University School of Medicine, Boston, Masssachusetts 02118, USA.
Jeanne C
JC
Latourelle
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
M Inmaculada
MI
Barrasa
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.
Johanna
J
Goldmann
Department of Neurology, Boston University School of Medicine, Boston, Masssachusetts 02118, USA.
Richard H
RH
Myers
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.|Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, Massachusetts 02139, USA.
Richard A
RA
Young
The Whitehead Institute, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.|Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, Massachusetts 02139, USA.
Rudolf
R
Jaenisch
D000483:Alleles; D001921:Brain / Q000378:metabolism; D064113:CRISPR-Cas Systems / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics; D005786:Gene Expression Regulation; D005818:Genetic Engineering; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D018398:Homeodomain Proteins / Q000378:metabolism; D006801:Humans; D008957:Models, Genetic; D010300:Parkinson Disease / Q000235:genetics*; D039904:Pluripotent Stem Cells / Q000378:metabolism; D012306:Risk; D014157:Transcription Factors / Q000378:metabolism; D051844:alpha-Synuclein / Q000235:genetics*; D000099260:Empty Spiracles Homeobox Proteins
D018398:Homeodomain Proteins; D014157:Transcription Factors; D051844:alpha-Synuclein; D000099260:Empty Spiracles Homeobox Proteins; C105201:NKX6-1 protein, human