Functional Characterization of Schizophrenia-Associated Variation in CACNA1C.
Calcium channel subunits, including CACNA1C, have been associated with multiple psychiatric disorders. Specifically, genome wide association studies (GWAS) have repeatedly identified the single nucleotide polymorphism (SNP) rs1006737 in intron 3 of CACNA1C to be strongly associated with schizophrenia and bipolar disorder. Here, we show that rs1006737 marks a quantitative trait locus for CACNA1C transcript levels. We test 16 SNPs in high linkage disequilibrium with rs1007637 and find one, rs4765905, consistently showing allele-dependent regulatory function in reporter assays. We find allele-specific protein binding for 13 SNPs including rs4765905. Using protein microarrays, we identify several proteins binding ≥3 SNPs, but not control sequences, suggesting possible functional interactions and combinatorial haplotype effects. Finally, using circular chromatin conformation capture, we show interaction of the disease-associated region including the 16 SNPs with the CACNA1C promoter and other potential regulatory regions. Our results elucidate the pathogenic relevance of one of the best-supported risk loci for schizophrenia and bipolar disorder.
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, United States of America.
Nicole
N
Eckart
Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, United States of America.
Qifeng
Q
Song
Psychiatry and Behavioral Sciences, Johns Hopkins Medicine, Baltimore, MD 21205, United States of America.
Rebecca
R
Yang
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, United States of America.
Ruihua
R
Wang
Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, United States of America.
Heng
H
Zhu
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, United States of America.
Andrew S
AS
McCallion
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, United States of America.|Psychiatry and Behavioral Sciences, Johns Hopkins Medicine, Baltimore, MD 21205, United States of America.
Dimitrios
D
Avramopoulos
D000328:Adult; D001714:Bipolar Disorder / Q000378:metabolism; D020746:Calcium Channels, L-Type / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics; D005260:Female; D057809:HEK293 Cells; D006801:Humans; D007438:Introns; D015810:Linkage Disequilibrium; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D040081:Protein Array Analysis; D017433:Protein Structure, Secondary; D012559:Schizophrenia / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
C079146:CACNA1C protein, human; D020746:Calcium Channels, L-Type