Functional analysis of polymorphisms in the promoter regions of genes on 22q11

Human Mutation

Volumn 24, Issue 1, 2004, Pages 35-42

  Hoogendoorn, Bastiaan ^a   Coleman, Sharon L ^a   Guy, Carol A ^a   Smith, S Kaye ^a   O'Donovan, Michael C ^a   Buckland, Paul R ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

Chromosome 22 deletion syndrome; DCGR14; GSTT2; PRODH; Promoter analysis; Schizophrenia; SERPIND1; SNP

Indexed keywords

DNA; MESSENGER RNA; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BIPOLAR DISORDER; CHROMOSOME 22Q; CHROMOSOME DELETION; CONTROLLED STUDY; DGCR14 GENE; DIGEORGE SYNDROME; DISEASE PREDISPOSITION; DKFZP434P211 GENE; GENE; GENE DOSAGE; GENETIC TRANSCRIPTION; GSTT2 GENE; HAPLOTYPE; HUMAN; HUMAN CELL; MENTAL DISEASE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PRODH GENE; PROMOTER REGION; REPORTER GENE; SCHIZOAFFECTIVE PSYCHOSIS; SCHIZOPHRENIA; SERPIND1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; VELOCARDIOFACIAL SYNDROME;

CELL LINE; CHROMOSOMES, HUMAN, PAIR 22; ETHNIC GROUPS; GENE EXPRESSION REGULATION; GENES; GENETIC SCREENING; GLUTATHIONE TRANSFERASE; HAPLOTYPES; HEPARIN COFACTOR II; HUMANS; KIDNEY; NUCLEAR PROTEINS; POLYMORPHISM, GENETIC; PROLINE OXIDASE; PROMOTER REGIONS (GENETICS); PROTEINS;

CUCUMBER MOSAIC VIRUS; FELIS CATUS;

EID: 3042824629     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20061     Document Type: Article

References (39)

1. Arinami T, Ohtsuki T, Takase K, Shimizu H, Yoshikawa T, Horigome H, Nakayama J, Toru M. 2001. Screening for 22q11 deletions in a schizophrenia population. Schizophr Res 52:167-170.
2. Bajic VB, Seah SH, Chong A, Krishnan SPT, Koh JLY, Brusic V. 2003. Computer model for recognition of functional transcription start sites in polymerase II promoters of vertebrates. J Mol Graph Model 21:323-332.
3. Bray NJ, Buckland PR, Williams NM, Williams HJ, Owen MJ, O'Donovan MC. 2003. A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain. Am J Hum Genet 73:152-161.
4. Burke TW, Kadonaga JT 1997. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 11:3020-3031.
5. Campbell HD, Webb GC, Young IG. 1997. A human homologue of the Drosophila melanogaster sluggish-A (proline oxidase) gene maps to 22q11.2, and is a candidate gene for type-I hyperprolinaemia. Hum Genet 101:69-74.
6. Chakravarti A. 2002. A compelling genetic hypothesis for a complex disease: PRODH/DGCR6 variation leads to schizophrenia susceptibility. Proc Natl Acad Sci USA 99:4755-4756.
7. Coleman SL, Hoogendoorn B, Guy C, Smith SK, O'Donovan MC, Buckland PR. 2002a. A streamlined approach to functional analysis of promoter polymorphisms. BioTechniques 33:412-418.
8. Coleman SL, Buckland PR, Hoogendoorn B, Guy C, Smith K, O'Donovan MC. 2002b. Experimental analysis of the annotation of promoters in the public database. Hum Mol Genet 11:1817-1821.
9. Frith MC, Hansen U, Weng Z. 2001. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17:878-889.
10. Gisler R, Sigvardsson M. 2002. The human V-preB promoter is a target for coordinated activation by early B cell factor and E47. J Immunol 168:5130-5138.
11. Gogos JA, Santha M, Takacs Z, Beck KD, Luine V, Lucas LR, Nadler JV, Karayiorgou M. 1999. The gene encoding proline dehydrogenase modulates sensorimotor gating in mice. Nat Genet 21:434-439.
12. Gong W, Emanuel BS, Galili N, Kim DH, Roe B, Driscoll DA, Budarf ML. 1997. Structural and mutational analysis of a conserved gene (DGSI) from the minimal DiGeorge syndrome critical region. Hum Mol Genet 6:267-276.
13. Goodman BK, Rutberg J, Lin WW, Pulver AE, Thomas GH. 2000. Hyperprolinaemia in patients with deletion (22)(q11.2) syndrome. J Inherit Metab Dis 23:847-848
14. Grabe N. 2002. AliBaba2: context specific identification of transcription factor binding sites. In Silico Biol 2S1-S1.
15. Hayes JD, Strange RC. 2000. Glutathione S-transferase polymorphisms and their biological consequences. Pharmacology 61:154-166.
16. Hoogendoorn B, Coleman SL, Guy CA, Smith SK, Bowen T, Buckland PR, O'Donovan MC. 2003. Functional analysis of human promoter polymorphisms. Hum Mol Genet 12:2249-2254.
17. Ivanov D, Kirov G, Norton N, Williams HJ, Williams NM, Nikolov I, Tzwetkova R, Stambolova SM, Murphy KC, Toncheva D, Thapar A, O'Donovan MC, Owen MJ. 2003. Chromosome 22q11 deletions, velo-cardio-facial syndrome and early-onset psychosis. Molecular genetic study. Br J Psychiatry 183:409-413.
18. Jones AC, Austin J, Hansen N, Hoogendoorn B, Oefner PJ, Cheadle JP, O'Donovan MC. 1999. Optimal temperature selection for mutation detection by denaturing HPLC and comparison to single-stranded conformation polymorphism and heteroduplex analysis. Clin Chem 45:1133-1140.
19. Lindsay EA, Botta A, Jurecic V, Carattini-Rivera S, Cheah YC, Rosenblatt HM, Bradley A, Baldini A. 1999. Congenital heart disease in mice deficient for the DiGeorge syndrome region. Nature 401:379-383.
20. Lindsay EA. 2001. Chromosomal microdeletions: dissecting de122q11 syndrome. Nat Rev Genet 2:858-868.
21. Liu H, Abecasis GR, Heath SC, Knowles A, Demars S, Chen YJ, Roos JL, Rapoport JL, Gogos JA, Karayiorgou M. 2002a. Genetic variation in the 22q11 locus and susceptibility to schizophrenia. Proc Natl Acad Sci USA 99:16859-16864.
22. Liu H, Heath SC, Sobin C, Roos JL, Galke BL, Blundell ML, Lenane M, Robertson B, Wijsman EM, Rapoport JL, Gogos JA, Karayiorgou M. 2002b. Genetic variation at the 22q11 PRODH2/DGCR6 locus presents an unusual pattern and increases susceptibility to schizophrenia. Proc Natl Acad Sci USA 99:3717-3722.
23. Liu R, States DJ. 2002. Consensus promoter identification in human genome utilizing expressed sequence markers and gene modeling. Genome Res 12:462-469.
24. McDermid HE, Morrow BE. 2002. Genomic disorders on 22q11. Am J Hum Genet 70:1077-1088.
25. Murphy K. 2002. Schizophrenia and velo-facial syndrome. Lancet 359:426-430.
26. Noda A, Wada H, Kusiya F, Sakakura M, Nakatani K, Gabazza EC, Asahara N, Tsukada M, Nobori T, Shiku H. 2002. Plasma levels of heparin cofactor II (HCII) and thrombin-HCII complex in patients with disseminated intravascular coagulation. Clin Appl Thromb Hemost 8:265-271.
27. Périer RC, Praz V, Junier T, Bonnard C, Bucher P. 2000. The Eukaryotic Promoter Database (EPD). Nucl Acids Res 28: 302-303.
28. Praz V, Périer RC, Bonnard C, Bucher P. 2002. The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucl Acids Res 30:322-324.
29. Pritchard JK. 2001. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69:124-137
30. Rizzu P, Lindsay EA, Taylor C, O'Donnell H, Levy A, Scrambler P, Baldini A. 1996. Cloning and comparative mapping of a gene from the commonly deleted region of DiGeorge and Velocardiofacial syndromes conserved in C. elegans. Mamm Genome 7:639-643
31. Rozen S, Skaletsky HJ. Primer3. 1998. Code available at http://wwwgenome.wi.mit.edu/genome_software/other/primer3.html
32. Shaikh TH, Kurahashi H, Emanuel BS. 2001. Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review. Genet Med 3:6-13.
33. Shifman S, Bronstein M, Sternfeld M, Pisante-Shalom A, Lev-Lehman E, Weizman A, Reznik I, Spivak B, Grisaru N, Karp L, Schiffer R, Kotler M, Strous RD, Swartz-Vanetik M, Knobler HY, Shinar E, Beckmann JS, Yakir B, Risch N, Zak NB, Darvasi A. 2002. A highly significant association between a COMT haplotype and schizophrenia. Am J Hum Genet 71:1296-1302.
34. Strange RC, Spiteri MA, Ramachandran S, Fryer AA. 2001. Glutathione-S-transferase family of enzymes. Mutat Res 482:21-26.
35. Sun QA, Zappacosta F, Factor VM, Wirth PJ, Hatfield DL, Gladyshev VN. 2001. Heterogeneity within animal thioredoxin reductases: evidence for alternative first exon splicing. J Biol Chem 276:3106-3114.
36. Trinklein ND, Aldred SJ, Saldanha AJ, Myers RM. 2003. Identification and functional analysis of human transcriptional promoters. Genome Res 13:308-312.
37. Villa P, Aznar J, Vaya A, Espana F, Ferrando F, Mira Y, Estelles A. 1999. Hereditary homozygous heparin cofactor II deficiency and the risk of developing venous thrombosis. Thromb Haemost 82:1011-1014.
38. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F. 2000. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28:316-319.
39. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW. 2002. Allelic variation in human gene expression. Science 297:1143.