Survey of Schizophrenia and Bipolar Disorder Candidate Genes using Chromatin Immunoprecipitation and Tiled Microarrays (ChIP-chip)

References

• Addington A.M., Gornick M., Sporn A.L., Gogtay N., Greenstein D., Lenane M., et al. Polymorphisms in the 13q33.2 gene G72/G30 are associated with childhood-onset schizophrenia and psychosis not otherwise specified. Biol Psychiatry 2004; 55(10)976–980
   Google Scholar
• Allen N. C., Bagade S., McQueen M. B., Ioannidis J. P., Kavvoura F. K., Khoury M. J., et al. Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database. Nat Genet 2008; 40(7)827–834
   PubMed Web of Science ®Google Scholar
• Allemand E., Batsche E., Muchardt C. Splicing, transcription, and chromatin: a menage a trois. Curr Opin Genet Dev 2008; 18: 145–151
   Google Scholar
• Barski A., Cuddapah S., Cui K., Roh T. Y., Schones D. E., Wang Z., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129: 823–837
   PubMed Web of Science ®Google Scholar
• Bernstein B. E., Humphrey E. L., Erlich R. L., Schneider R., Bouman P., Liu J. S., et al. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA 2002; 99: 8695–8700
   PubMed Web of Science ®Google Scholar
• Bernstein B. E., Kamal M., Lindblad-Toh K., Bekiranov S., Bailey D. K., Huebert D. J., et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 2005; 120: 169–181
   PubMed Web of Science ®Google Scholar
• Bernstein B. E., Mikkelsen T. S., Xie X., Kamal M., Huebert D. J., Cuff J., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006; 125: 315–326
   PubMed Web of Science ®Google Scholar
• Bray N. J., Preece A., Williams N. M., Moskvina V., Buckland P. R., Owen M. J., et al. Haplotypes at the dystrobrevin-binding protein 1 (DTNBP1) gene locus mediate risk for schizophrenia through reduced DTNBP1 expression. Hum Mol Genet 2005; 14: 1947–1954
   PubMed Web of Science ®Google Scholar
• Breen G., Prata D., Osborne S., Munro J., Sinclair M., Li T., et al. Association of the dysbindin gene with bipolar affective disorder. Am J Psychiatry 2006; 163: 1636–1638
   PubMedGoogle Scholar
• Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997; 268(1)78–94
   PubMed Web of Science ®Google Scholar
• Callicott J. H., Straub R. E., Pezawas L., Egan M. F., Mattay V. S., Hariri A. R., et al. Variation in DISC1 affects hippocampal structure and function and increases risk for schizophrenia. Proc Natl Acad Sci U S A 2005; 102: 8627–8632
   PubMed Web of Science ®Google Scholar
• Chen K., Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 2007; 8: 93–103
   PubMed Web of Science ®Google Scholar
• Chen X., Wang X., O'Neill A. F., Walsh D., Kendler K. S. Variants in the catechol-O-methyltransferase (COMT) gene are associated with schizophrenia in Irish high-density families. Mol Psychiatry 2004; 9: 962–967
   PubMedGoogle Scholar
• Chubb J. E., Bradshaw N. J., Soares D. C., Porteous D. J., Millar J. K. The DISC locus in psychiatric illness. Mol Psychiatry 2008; 13(1)36–64
   PubMed Web of Science ®Google Scholar
• Corvin A., Donohoe G., Nangle J. M., Schwaiger S., Morris D., Gill M. A dysbindin risk haplotype associated with less severe manic-type symptoms in psychosis. Neurosci Lett 2008; 431(2)146–149
   Google Scholar
• Corvin A., McGhee K. A., Murphy K., Donohoe G., Nangle J. M., Schwaiger S., et al. Evidence for association and epistasis at the DAOA/G30 and D-amino acid oxidase loci in an Irish schizophrenia sample. Am J Med Genet B (Neuropsychiatr Genet) 2007; 144(7)949–953
   Google Scholar
• De Luca V., Voineskos D., Shinkai T., Wong G., Kennedy J. L. Untranslated region haplotype in dysbindin gene: analysis in schizophrenia. J Neural Transm 2005; 112: 1263–1267
   Google Scholar
• Farmer A., Elkin A., McGuffin P. The genetics of bipolar affective disorder. Curr Opin Psychiatry 2007; 20: 8–12
   Google Scholar
• Fatemi S. H., King D. P., Reutiman T. J., Folsom T. D., Laurence J. A., Lee S., et al. PDE4B polymorphisms and decreased PDE4B expression are associated with schizophrenia. Schizophr Res 2008; 101(1–3)38–49
   Google Scholar
• Follows G. A., Dhami P., Gottgens B., Bruce A. W., Campbell P. J., Dillon S. C., et al. Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites. Genome Res 2006; 16: 1310–1319
   Google Scholar
• Georgieva L., Dimitrova A., Ivanov D., Nikolov I., Williams N.M., Grozeva D., et al. Support for neuregulin 1 as a susceptibility gene for bipolar disorder and schizophrenia. Biol Psychiatry 2008; 64(5)419–427
   Google Scholar
• Harrison P. J., Weinberger D. R. Schizophrenia genes, gene expression, and neuropathology: on the matter of their convergence. Mol Psychiatry 2005; 10: 40–68
   PubMed Web of Science ®Google Scholar
• Hattori E., Liu C., Badner J.A., Bonner T.I., Christian S.L., Maheshwari M., et al. Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with bipolar disorder in two independent pedigree series. Am J Hum Genet 2003; 72(5)1131–1140
   Google Scholar
• Heintzman N. D., Stuart R. K., Hon G., Fu Y., Ching C. W., Hawkins R. D., et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Gen 2007; 9: 311–318
   Google Scholar
• Hennah W., Varilo T., Kestilä M., Paunio T., Arajärvi R., Haukka J., et al. Haplotype transmission analysis provides evidence of association for DISC1 to schizophrenia and suggests sex-dependent effects. Hum Mol Genet 2003; 12: 3151–3159
   PubMed Web of Science ®Google Scholar
• Hennah W., Thomson P., Peltonen L., Porteous D. Genes and schizophrenia: beyond schizophrenia: the role of DISC1 in major mental illness. Schizophr Bull 2006; 32: 409–416
   PubMed Web of Science ®Google Scholar
• Hennah, W., Thomson, P., McQuillin, A., Bass, N., Loukola, A., Anjorin, A., , et al. 2008. DISC1 association, heterogeneity, and interplay in schizophrenia and bipolar disorder. Mol Psychiatry, [Epub ahead of print] March 4 2008.
   Google Scholar
• Ivaldi M. S., Karam C. S., Corces V. G. Phosphorylation of histone H3 at Ser10 facilitates RNA polymerase II release from promoter-proximal pausing in drosophila. Genes Dev 2007; 21: 2818–2831
   PubMed Web of Science ®Google Scholar
• Kamiya A., Kubo K., Tomoda T., Takaki M., Youn R., Ozeki Y., et al. A schizophrenia-associated mutation of DISC1 perturbs cerebral cortex development. Nat Cell Biol 2005; 7(12)1167–1178
   PubMed Web of Science ®Google Scholar
• Kéri, S., Kiss, I., Seres, I., Kelemen, O. 2008. A polymorphism of the neuregulin 1 gene (SNP8NRG243177/rs6994992) affects reactivity to expressed emotion in schizophrenia. Am J Med Genet B Neuropsychiatr Genet, [Epub ahead of print] June 9 2008.
   Google Scholar
• Kilpinen H., Ylisaukko-Oja T., Hennah W., Palo O. M., Varilo T., Vanhala R., et al. Association of DISC1 with autism and Asperger syndrome. Mol Psychiatry 2008; 13(2)187–196
   PubMed Web of Science ®Google Scholar
• Kim A., Kiefer C. M., Dean A. Distinctive signatures of histone methylation in transcribed coding and noncoding human beta-globin sequences. Mol Cell Biol 2007; 27: 1271–1279
   PubMed Web of Science ®Google Scholar
• Kim T. J., Kraus J. C., Chen J., Lee Y. Jumonji, a critical factor for cardiac development functions as a transcriptional repressor. J Biol Chem 2003; 278: 42247–42255
   PubMed Web of Science ®Google Scholar
• Kishimoto M., Ujike H., Motohashi Y., Tanaka Y., Okahisa Y., Kotaka T., et al. The dysbindin gene (DTNBP1) is associated with methamphetamine psychosis. Biol Psychiatry 2008; 63(2)191–196
   Google Scholar
• Kornberg R. D., Lorch Y. Chromatin-modifying and -remodeling complexes. Curr Opin Genet Dev 1999; 9: 148–151
   PubMed Web of Science ®Google Scholar
• Lachman H. M., Pedrosa E., Petruolo O. A., Cockerham M., Papolos A., Novak T., et al. Increase in GSK3 gene copy number variation in bipolar disorder. Am J Med Genet B (Neuropsychiatr Genet) 2007; 144: 259–265
   Google Scholar
• Law A. J., Lipska B. K., Weickert C. S., Hyde T. M., Straub R. E., Hashimoto R., et al. Neuregulin 1 transcripts are differentially expressed in schizophrenia and regulated by 5’ SNPs associated with the disease. Proc Natl Acad Sci U S A 2006; 103: 6747–6752
   PubMed Web of Science ®Google Scholar
• Lemon B., Tjian R. Orchestrated response: a symphony of transcription actors for gene control. Genes Dev 2000; 14: 2551–2569
   PubMed Web of Science ®Google Scholar
• Li T., Stefansson H., Gudfinnsson E., Cai G., Liu X., Murray R. M., et al. Identification of a novel neuregulin 1 at-risk haplotype in Han schizophrenia Chinese patients, but no association with the Icelandic/Scottish risk haplotype. Mol Psychiatry 2004; 9: 698–704
   PubMedGoogle Scholar
• Li T., Zhang F., Liu X., Sun X., Sham P. C., Crombie C., et al. Identifying potential risk haplotypes for schizophrenia at the DTNBP1 locus in Han Chinese and Scottish populations. Mol Psychiatry 2005; 10(11)1037–1044
   PubMedGoogle Scholar
• Maeda K., Nwulia E., Chang J., Balkissoon R., Ishizuka K., Chen H., et al. Differential expression of disrupted-in-schizophrenia (DISC1) in bipolar disorder. Biol Psychiatry 2006; 60: 929–935
   Google Scholar
• McIntosh A.M., Moorhead T.W., Job D., Lymer G.K., Muñoz Maniega S., McKirdy J., et al. The effects of a neuregulin 1 variant on white matter density and integrity. Mol Psychiatry 2008; 13(11)1054–1059
   Google Scholar
• Millar J. K., Pickard B. S., Mackie S., James R., Christie S., Buchanan S. R., et al. DISC1 and PDE4B are interacting genetic factors in schizophrenia that regulate cAMP signaling. Science 2005; 310(5751)1187–1191
   PubMed Web of Science ®Google Scholar
• Numata, S., Ueno, S., I., Iga, J., I., Song, H., Nakataki, M., Tayoshi, S., , et al. 2008. Positive association of the PDE4B (phosphodiesterase 4B) gene with schizophrenia in the Japanese population. J Psychiatr Res, [Epub ahead of print].
   Google Scholar
• Nielsen K. B., Sorensen S., Cartegni L., Corydon T. J., Doktor T. K., Schroeder L. D., et al. Seemingly neutral polymorphic variants may confer immunity to splicing_inactivating mutations: a synonymous SNP in Exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. Am J Hum Genet 2007; 80: 416–432
   PubMed Web of Science ®Google Scholar
• Norton N., Williams H. J., Owen M.J. An update on the genetics of schizophrenia. Curr Opin Psychiatry 2006; 19(2)158–164
   PubMedGoogle Scholar
• Oberley M. J., Tsao J., Yau P., Farnham P. J. High-throughput screening of chromatin immunoprecipitates using CpG-island microarrays. Meth Enzymol 2004; 376: 315–334
   PubMedGoogle Scholar
• Pae C. U., Serretti A., Mandelli L., Yu H. S., Patkar A. A., Lee C. U., et al. Effect of 5-haplotype of dysbindin gene (DTNBP1) polymorphisms for the susceptibility to bipolar I disorder. Am J Med Genet B (Neuropsychiatr Genet) 2007; 144: 701–703
   Google Scholar
• Pagani F., Raponi M., Baralle F. E. Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci USA 2005; 102: 6368–6372
   PubMed Web of Science ®Google Scholar
• Palo O. M., Antila M., Silander K., Hennah W., Kilpinen H., Soronen P., et al. Association of distinct allelic haplotypes of DISC1 with psychotic and bipolar spectrum disorders and with underlying cognitive impairments. Hum Mol Genet 2007; 16(20)2517–2528
   PubMed Web of Science ®Google Scholar
• Pedrosa E., Ye K., Nolan K. A., Morrell L., Okum J. M., Persky A. D., et al. Positive association of schizophrenia to JARID2 gene. Am J Med Genet B (Neuropsychiatr Genet) 2007; 144: 45–51
   Google Scholar
• Pedrosa E., Stefanescu R., Petruolo O., Lo Y., Nolan K., Stopkova P., et al. Analysis of protocadherin alpha gene enhancer polymorphism in bipolar disorder and schizophrenia. Schizophr Res 2008; 102(1–3)210–219
   Google Scholar
• Pennacchio L. A., Ahituv N., Moses A. M., Prabhakar S., Nobrega M. A., Shoukry M., et al. In vivo enhancer analysis of human conserved noncoding sequences. Nature 2007; 444(7118)499–502
   Google Scholar
• Petryshen T. L., Middleton F. A., Kirby A., Aldinger K. A., Purcell S., Tahl A. R., et al. Support for involvement of neuregulin 1 in schizophrenia pathophysiology. Mol Psychiatry 2005; 10: 366–374
   PubMed Web of Science ®Google Scholar
• Prata, D. , Breen, G. , Osborne, S. , Munro, J. , St. Clair, D. , Collier, D. 2008. Association of DAO and G72(DAOA)/G30 genes with bipolar affective disorder. Am J Med Genet B (Neuropsychiatr Genet), [Epub ahead of print].
   Google Scholar
• Qu H. Q., Lawrence S. G., Guo F., Majewski J., Polychronakos C. Strand bias in complementary single-nucleotide polymorphisms of transcribed human sequences: evidence for functional effects of synonymous polymorphisms. BMC Genom 2006; 7: 213
   Google Scholar
• Raybould R., Green E. K., MacGregor S., Gordon-Smith K., Heron J., Hyde S., et al. Bipolar disorder and polymorphisms in the dysbindin gene (DTNBP1). Biol Psychiatry 2005; 57: 696–701
   Google Scholar
• Ribich S., Tasic B., Maniatis T. Identification of long-range regulatory elements in the protocadherin {alpha} gene cluster. Proc Natl Acad Sci U S A 2006; 103(52)19719–19724
   Google Scholar
• Roh T. Y., Cuddapah S., Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 2005; 19: 542–552
   PubMed Web of Science ®Google Scholar
• Roh T. Y., Ngau W. C., Cui K., Landsman D., Zhao K. High-resolution genome-wide mapping of histone modifications. Nat Biotechnol 2004; 22: 1013–1016
   PubMed Web of Science ®Google Scholar
• Roh T. Y., Wei G., Farrell C. M., Zhao K. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res 2007; 7: 74–81
   Google Scholar
• Schwab S. G., Knapp M., Mondabon S., Hallmayer J., Borrmann-Hassenbach M., Albus M., et al. Support for association of schizophrenia with genetic variation in the 6p22.3 gene, dysbindin, in sib-pair families with linkage and in an additional sample of triad families. Am J Hum Genet 2003; 72: 185–190
   PubMed Web of Science ®Google Scholar
• Serretti A., Mandelli L. The genetics of bipolar disorder: genome “hot regions,” genes, new potential candidates, and future directions. Mol Psychiatry 2008; 13(8)742–771
   Google Scholar
• Shi J., Badner J. A., Gershon E. S., Liu C. Allelic association of G72/G30 with schizophrenia and bipolar disorder: a comprehensive meta-analysis. Schizophr Res 2008; 98(1–3)89–97
   Google Scholar
• Stanke M., Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003; 19(Suppl. 2)215–225
   Google Scholar
• St. Clair D., Blackwood D., Muir W., Carothers A., Walker M., Spowart G., et al. Association within a family of a balanced autosomal translocation with major mental illness. Lancet 1990; 336(8706)13–16
   PubMed Web of Science ®Google Scholar
• Stefansson H., Sarginson J., Kong A., Yates P., Steinthorsdottir V., Gudfinnsson E., et al. Association of neuregulin 1 with schizophrenia confirmed in Scottish population. Am J Hum Genet 2003; 72: 83–87
   PubMed Web of Science ®Google Scholar
• Stefansson H., Sigurdsson E., Steinthorsdottir V., Bjornsdottir S., Sigmundsson T., Ghosh S., et al. Neuregulin 1 and susceptibility to schizophrenia. Am J Hum Genet 2002; 71: 877–892
   PubMed Web of Science ®Google Scholar
• Steinthorsdottir V., Stefansson H., Ghosh S., Birgisdottir B., Bjornsdottir S., Fasquel A. C., et al. Multiple novel transcription initiation sites for NRG1. Gene 2004; 342: 97–105
   Google Scholar
• Straub R. E., Jiang Y., MacLean C. J., Ma Y., Webb B. T., Myakishev M. V., et al. Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia. Am J Hum Genet 2002; 71: 337–348
   PubMed Web of Science ®Google Scholar
• Sun, J. , Kuo, P. H. , Riley, B. P. , Kendler, K. S. , Zhao, Z. 2008. Candidate genes for schizophrenia: a survey of association studies and gene ranking. Am J Med Genet B (Neuropsychiatr Genet), [Epub ahead of print].
   Google Scholar
• Takahashi M., Shimodaira H., Andreutti-Zaugg C., Iggo R., Kolodner R. D., Ishioka C. Functional analysis of human MLH1 variants using yeast and in vitro mismatch repair assays. Cancer Res 2007; 67: 4595–4604
   PubMed Web of Science ®Google Scholar
• Tan W., Wang Y., Gold B., Chen J., Dean M., Harrison P. J., et al. Molecular cloning of a brain-specific, developmentally regulated Neuregulin 1 (NRG1) isoform, and identification of a functional promoter variant associated with schizophrenia. J Biol Chem 2007; 282(33)24343–24351
   PubMedGoogle Scholar
• Taylor M. S., Devon R. S., Millar J. K., Porteous D. J. Evolutionary constraints on the Disrupted-in-Schizophrenia locus. Genomics 2003; 81: 67–77
   PubMed Web of Science ®Google Scholar
• Thomson P. A., Christoforou A., Morris S. W., Adie E., Pickard B. S., Porteous D. J., et al. Association of neuregulin 1 with schizophrenia and bipolar disorder in a second cohort from the Scottish population. Mol Psychiatry 2007; 12(1)94–104
   Google Scholar
• Tosato S., Ruggeri M., Bonetto C., Bertani M., Marrella G., Lasalvia A., et al. Association study of dysbindin gene with clinical and outcome measures in a representative cohort of Italian schizophrenic patients. Am J Med Genet B (Neuropsychiatr Genet) 2007; 144B(5)647–659
   Google Scholar
• Walss-Bass C., Liu W., Lew D. F., Villegas R., Montero P., Dassori A., et al. A novel missense mutation in the transmembrane domain of neuregulin 1 is associated with schizophrenia. Biol Psychiatry 2006; 60: 548–553
   PubMedGoogle Scholar
• Wang X., He G., Gu N., Yang J., Tang J., Chen Q., et al. Association of G72/G30 with schizophrenia in the Chinese population.Biochem. Biophys Res Commun 2004; 19(4)1281–1286
   Google Scholar
• West A. G., Fraser P. Remote control of gene transcription. Hum Mol Genet 2005; 14(Spec No. 1)R101–R111
   PubMedGoogle Scholar
• Whetstine J. R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., et al. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 2006; 125: 467–481
   PubMed Web of Science ®Google Scholar
• Williams N. M., Preece A., Morris D. W., Spurlock G., Bray N. J., Stephens M., et al. Identification in two independent samples of a novel schizophrenia risk haplotype of the dystrobrevin binding protein gene (DTNBP1). Arch Gen Psychiatry 2004; 61: 336–344
   PubMedGoogle Scholar
• Williams N. M., Green E. K., Macgregor S., Dwyer S., Norton N., Williams H. Variation at the DAOA/G30 locus influences susceptibility to major mood episodes but not psychosis in schizophrenia and bipolar disorder. Arch Gen Psychiatry 2006; 63(4)366–373
   Google Scholar
• Wood L. S., Pickering E. H., Dechairo B. M. Significant support for DAO as a schizophrenia susceptibility locus: examination of five genes putatively associated with schizophrenia. Biol Psychiatry 2007; 61(10)1195–1199
   Google Scholar
• Xu X., Bieda M., Jin V. X., Rabinovich A., Oberley M. J., Green R., et al. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res 2007; 17(11)1550–1561
   Google Scholar
• Yang J. Z., Si T. M., Ruan Y., Ling Y. S., Han Y. H., Wang X. L., et al. Association study of neuregulin 1 gene with schizophrenia. Mol Psychiatry 2003; 8: 706–709
   PubMed Web of Science ®Google Scholar
• Yue W., Liu Z., Kang G., Yan J., Tang F., Ruan Y., et al. Association of G72/G30 polymorphisms with early-onset and male schizophrenia. Neuroreport 2006; 17(18)1899–1902
   Google Scholar