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The Dystrobrevin-Binding Protein 1 Gene

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The Dystrobrevin-Binding Protein 1 Gene Molecular Psychiatry (2009) 14,18–29 & 2009 Nature Publishing Group All rights reserved 1359-4184/09 $32.00 www.nature.com/mp FEATURE REVIEW The dystrobrevin-binding protein 1 gene: features and networks AY Guo1,4, J Sun1,4, BP Riley1,2, DL Thiselton1, KS Kendler1,2 and Z Zhao1,2,3 1Department of Psychiatry and Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, Richmond, VA, USA; 2Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA and 3Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA The dystrobrevin-binding protein 1 (DTNBP1) gene has been one of the most studied and promising schizophrenia susceptibility genes since it was first reported to be associated with schizophrenia in the Irish Study of High Density Schizophrenia Families (ISHDSF). Although many studies have been performed both at the functional level and in association with psychiatric disorders, there has been no systematic review of the features of the DTNBP1 gene, protein or the relationship between function and phenotype. Using a bioinformatics approach, we identified the DTNBP1 gene in 13 vertebrate species. The comparison of these genes revealed a conserved gene structure, protein-coding sequence and dysbindin domain, but a diverse noncoding sequence. The molecular evolutionary analysis suggests the DTNBP1 gene probably originated in chordates and matured in vertebrates. No signature of recent positive selection was seen in any primate lineage. The DTNBP1 gene likely has many more alternative transcripts than the current three major isoforms annotated in the NCBI database. Our examination of risk haplotypes revealed that, although the frequency of a single nucleotide polymorphism (SNP) or haplotype might be significantly different in cases from controls, difference between major geographic populations was even larger. Finally, we constructed the first DTNBP1 interactome and explored its network features. Besides the biogenesis of lysosome-related organelles complex 1 and dystrophin-associated protein complex, several molecules in the DTNBP1 network likely provide insight into the role of DTNBP1 in biological systems: retinoic acid, b-estradiol, calmodulin and tumour necrosis factor. Studies of these subnetworks and pathways may provide opportunities to deepen our understanding of the mechanisms of action of DTNBP1 variants. Molecular Psychiatry (2009) 14, 18–29; doi:10.1038/mp.2008.88; published online 29 July 2008 Keywords: DTNBP1; schizophrenia; splicing; haplotype; protein–protein interaction; gene network Introduction In 2002, Straub et al.6 first identified the DTNBP1 gene as a putative schizophrenia susceptibility gene The human dystrobrevin-binding protein 1 (DTNBP1) by undertaking systematic linkage disequilibrium gene spans B140 kb on chromosome 6p22.3 and has mapping across a linkage region on 6p in the 270 10 exons. So far, it has not yet been classified into any multiply affected pedigrees from the Irish Study of known gene family. Dysbindin, a coiled-coil-contain- High Density Schizophrenia Families (ISHDSF). ing protein encoded by DTNBP1, was initially found Reanalysis of this data identified a single high-risk to interact with a- and b-dystrobrevin (DTNA and haplotype containing 8 single nucleotide polymorph- DTNB) in the muscle and brain of mice.1 DTNA and isms (SNPs) covering 30 kb.7 As of 19 April 2008, 45 DTNB are members of the dystrophin-associated follow-up association studies, 18 of which had protein complex (DPC), which links the cytoskeleton positive results, are annotated in the Schizophrenia- to the extracellular matrix and serves as a scaffold for Gene database.8 One meta-analysis has been pub- signaling proteins.1,2 Dysbindin is also an essential lished.9 So far, DTNBP1 has been one of the most component of the biogenesis of lysosome-related prominent schizophrenia susceptibility genes.10,11 organelles complex 1 (BLOC-1) and interacts with DTNBP1 has been associated with other phenotypes all seven other components of BLOC-1.3–5 including intelligence, schizoaffective disorder, bipo- lar disorder and the Hermansky–Pudlak syndrome Correspondence: Dr Z Zhao, Department of Psychiatry, Virginia type 7.3,12,13 Commonwealth University, 800 East Leigh Street, Suite 118, DTNBP1 association studies have been frequently Richmond, VA 23298, USA. cited and reviewed,10,14–16 and will not be discussed E-mail: [email protected] 4These authors contributed equally to this work. here. However, its gene feature, expression and Received 13 May 2008; revised 24 June 2008; accepted 2 July protein’s interactions with other molecules in cellular 2008; published online 29 July 2008 systems have largely remained speculative.14 For DTNBP1 gene features and networks AY Guo et al 19 Table 1 DTNBP1 gene in 13 species Species Gene ID DNA CDS Amino Dysbindin Major acid domain source Length Repeat a Length Identityb Length Identityb Length Identityb (kb) (%) (bp) (%) (aa) (%) (aa) (%) Human 84062 140.2 52.8 1056 351 121 NCBI Chimp ENSPTRG00000017744 145.9 50.8 1002 99.0 333 99.4 121 99.2 Ensembl Orangutanc 143.5 49.5 1050 98.1 349 97.7 121 100.0 Genome Rhesus ENSMMUG00000015363 147.1 52.0 996 97.3 331 97.3 120 97.5 Ensembl Marmostc 137.4 45.8 1056 95.1 351 94.3 121 94.2 Genome Dog ENSCAFG00000009893 115.8 40.9 1026 79.7 341 78.6 121 78.5 Ensembl Pig 100049697 118.4 39.0 1029 83.4 342 84.6 121 80.2 NCBI Cow 506612 89.1 38.0 1029 84.3 342 85.2 121 84.3 NCBI Mouse 94245 80.0 28.3 1059 83.0 352 77.7 121 80.2 NCBI Rat 641528 90.4 30.9 1059 81.8 352 76.8 121 81.0 NCBI Opossum ENSMODG00000010762 207.0 1038 79.2 345 82.1 120 81.8 Ensembl Chicken 420840 68.7 7.8 1056 76.4 351 78.5 121 87.6 NCBI Zebrafish 394109 31.1 22.5 1089 67.9 362 63.2 124 68.6 NCBI Abbreviations: chimp, chimpanzee; rhesus, rhesus macaque. aThe proportion (%) of repetitive sequences identified by the RepeatMasker. bIdentity was calculated by comparing with the human DTNBP1 sequence. cOrangutan and marmost DTNBP1 genes were predicted from their draft genomes (see Supplementary Materials and methods). example, there are few amino acid changes (nonsy- extensive search for the DTNBP1 gene in several nonymous mutations) observed in the human popula- major databases including NCBI Entrez Gene, tion, none of which has been reported to be associated Ensembl and dbEST, as well as in all the available with schizophrenia. Recent studies revealed a re- genomes (see Supplementary Materials and methods). duced expression of DTNBP1 in the frontal cortex and Based on these sources, we identified human hippocampal formation of schizophrenia patients.17–19 DTNBP1 orthologs in 12 other vertebrates, including DTNBP1 may confer susceptibility to schizophrenia 4 non-human primates, 6 non-primate mammals, and via reduced expression mediated by its high risk 2 non-mammals (Table 1). The length of its amino haplotype, which might tag one or more cis-acting acid sequence is 351 in humans. Similar length and variants.17,20 These observations call for an investiga- high identity of the amino acids are observed in other tion of the functional elements or regulatory mechan- species (Table 1). A dysbindin domain is annotated isms which might affect the DTNBP1 expression and (positions 184–304 in NCBI human dysbindin isoform confer the illness. Importantly, protein–protein a, NP_115498). The domain is highly conserved interaction (PPI) analysis of DISC1 (Disrupted in among the vertebrates. For example, the identity Schizophrenia 1), another prominent schizophrenia is 87.6% between human and chicken dysbindin susceptibility gene, suggested that schizophrenia domains. susceptibility genes (for example, DTNBP1 and Gene structure is also similar across species. DISC1) may share common PPIs and affect common For example, 10 exons are annotated in the databases biological processes.21 If this is true, network analysis or have been consistently predicted in the 13 species. may reveal novel mechanisms of etiology and inter- However, gene length varies widely from 31.1 kb in vention not easily reached by more conventional zebrafish to 207.0 kb in opossums, probably as a result approaches (for example, single gene analysis). of variation in the extent of repeats. For example, Here, we apply bioinformatics and systems biology human DTNBP1 has 74 088 bp repetitive sequences, approaches to explore the features of DTNBP1, accounting for 52.8% of the sequence; conversely, including its molecular evolution and sequence mouse DTNBP1 has 22 648 bp repetitive sequences, conservation, gene structure, transcripts, haplotypes accounting for only 28.3% of the sequence (Supple- and interactome and pathways. mentary Table S1). Repeats account for a smaller proportion in chickens and zebrafish DTNBP1 genes, whose lengths are also shorter. Conserved DTNBP1 gene structure in vertebrates Figure 1 shows the aligned amino acid sequences and protein features in the 13 species. Overall, the So far, the DTNBP1 gene has only been experimen- coiled-coil region, dysbindin domain, and some other tally verified in mice1 and humans.6 We performed an functional sites are conserved among these species. Molecular Psychiatry DTNBP1 gene features and networks AY Guo et al 20 The N-terminal region is more conserved than mentary Table S2; Supplementary Figure S2). When the C-terminal region. Phylogenetic trees were more genetically distant species (human, dog, mouse, reconstructed using the aligned amino acid sequences and opossum) were employed
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