Fine-mapping reveals novel alternative splicing of the dopamine transporter.
The dopamine transporter gene (SLC6A3, DAT) has been implicated in the pathogenesis of numerous psychiatric and neurodevelopmental disorders, including schizophrenia (SZ). We previously detected association between SZ and intronic SLC6A3 variants that replicated in two independent Caucasian samples, but had no obvious function. In follow-up analyses, we sequenced the coding and intronic regions of SLC6A3 to identify complete linkage disequilibrium patterns of common variations. We genotyped 78 polymorphisms, narrowing the potentially causal region to two correlated clusters of associated SNPs localized predominantly to introns 3 and 4. Our computational analysis of these intronic regions predicted a novel cassette exon within intron 3, designated E3b, which is conserved among primates. We confirmed alternative splicing of E3b in post-mortem human substantia nigra (SN). As E3b introduces multiple in-frame stop codons, the SLC6A3 open reading frame is truncated and the spliced product may undergo nonsense mediated decay. Thus, factors that increase E3b splicing could reduce the amount of unspliced product available for translation. Observations consistent with this prediction were made using cellular assays and in post-mortem human SN. In mini-gene constructs, the extent of splicing is also influenced by at least two common haplotypes, so the alternative splicing was evaluated in relation to SZ risk. Meta-analyses across genome-wide association studies did not support the initial associations and further post-mortem studies did not suggest case-control differences in splicing. These studies do not provide a compelling link to schizophrenia. However, the impact of the alternative splicing on other neuropsychiatric disorders should be investigated. © 2010 Wiley-Liss, Inc.
Talkowski
Michael E
ME
Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
McCann
Kathleen L
KL
Chen
Michael
M
McClain
Lora
L
Bamne
Mikhil
M
Wood
Joel
J
Chowdari
Kodavali V
KV
Watson
Annie
A
Prasad
Konasale M
KM
Kirov
George
G
Georgieva
Lyudmilla
L
Toncheva
Draga
D
Mansour
Hader
H
Lewis
David A
DA
Owen
Michael
M
O'Donovan
Michael
M
Papasaikas
Panagiotis
P
Sullivan
Patrick
P
Ruderfer
Douglas
D
Yao
Jeffrey K
JK
Leonard
Sherry
S
Thomas
Pramod
P
Miyajima
Fabio
F
Quinn
John
J
Lopez
A Javier
AJ
Nimgaonkar
Vishwajit L
VL
D000483:Alleles; D017398:Alternative Splicing; D001483:Base Sequence; D050483:Dopamine Plasma Membrane Transport Proteins / Q000235:genetics*; D005091:Exons; D005260:Female; D005787:Gene Frequency; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007438:Introns; D015810:Linkage Disequilibrium; D008297:Male; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012559:Schizophrenia / Q000235:genetics* / Q000378:metabolism; D013378:Substantia Nigra / Q000378:metabolism
D050483:Dopamine Plasma Membrane Transport Proteins; C493214:SLC6A3 protein, human