In silico detection of sequence variations modifying transcriptional regulation

PLoS Computational Biology

Volumn 4, Issue 1, 2008, Pages 0043-0054

  Andersen, Malin C ^a,b   Engström, Pär G ^c,d   Lithwick, Stuart ^e,f   Arenillas, David ^f   Eriksson, Per ^b   Lenhard, Boris ^c   Wasserman, Wyeth W ^f   Odeberg, Jacob ^a,b  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^c UNIVERSITY OF BERGEN   (Norway)

^d KAROLINSKA INSTITUTE   (Sweden)

^e UNIVERSITY OF TORONTO   (Canada)

^f UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; BINDING SITES; PHYLOGENETIC; SITE SELECTION; TRANSCRIPTION; TRANSCRIPTION FACTORS;

ANALYSIS OF VARIATIONS; BINDING SITE PREDICTIONS; BIOCHEMICAL MECHANISMS; COMPLEX DISEASE; GENETIC VARIATION; IN-SILICO; REGULATORY ANALYSIS; REGULATORY SEQUENCES; SEQUENCE VARIATIONS; TRANSCRIPTIONAL REGULATION;

FORECASTING;

ALPHA FETOPROTEIN; ALPHA GLOBIN; TRANSCRIPTION FACTOR;

ALPHA THALASSEMIA; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SYSTEM; GENE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE MUTATION; GENETIC LINKAGE; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; NONHUMAN; PHYLOGENY; PREDICTION; RAVEN SYSTEM; RNA ANALYSIS; TRANSCRIPTION REGULATION; UGTIA1 GENE; ALGORITHM; DNA SEQUENCE; GENETICS; INTERNET; METHODOLOGY; PROTEIN BINDING; REGULATORY SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BINDING SITES; GENETIC VARIATION; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN BINDING; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 38949195057     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0040005     Document Type: Article

References (50)

1. Kuriki C, Tanaka T, Fukui Y, Sato O, Motojima K (2002) Structural and functional analysis of a new upstream promoter of the human FAT/CD36 gene. Biol Pharm Bull 25: 1476-1478.
2. Zabetian CP, Anderson GM, Buxbaum SG, Elston RC, Ichinose H, et al. (2001) A quantitative-trait analysis of human plasma-dopamine beta-hydroxylase activity: evidence for a major functional polymorphism at the DBH locus. Am J Hum Genet 68: 515-522.
3. Rigat B, Hubert C, Alhenc-Gelas F, Cambien F, Corvol P, et al. (1990) An insertion/deletion polymorphism in the angiotensin I-converting enzyme gene accounting for half the variance of serum enzyme levels. J Clin Invest 86: 1343-1346.
4. Bosma PJ, Chowdhury JR, Bakker C, Gantla S, de Boer A, et al. (1995) The genetic basis of the reduced expression of bilirubin UDP-glucuronosyl- transferase 1 in Gilbert's syndrome. N Engl J Med 333: 1171-1175.
5. De Gobbi M, Viprakasit V, Hughes JR, Fisher C, Buckle VJ, et al. (2006) A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 312: 1215-1217.
6. Alj Y, Georgiakaki M, Savouret JF, Mal F, Attali P, et al. (2004) Hereditary persistence of alpha-fetoprotein is due to both proximal and distal hepatocyte nuclear factor-1 site mutations. Gastroenterology 126: 308-317.
7. Dawson S, Wiman B, Hamsten A, Green F, Humphries S, et al. (1993) The two allele sequences of a common polymorphism in the promoter of the plasminogen activator inhibitor-1 (PAI-1) gene respond differently to interleukin-1 in HepG2 cells. J Biol Chem 268: 10739-10745.
8. Grant PJ, Humphries SE (1999) Genetic determinants of arterial thrombosis. Baillieres Best Pract Res Clin Haematol 12: 505-532.
9. Jormsjö S, Ye S, Moritz J, Walter DH, Dimmeler S, et al. (2000) Allele-specific regulation of matrix metalloproteinase-12 gene activity is associated with coronary artery luminal dimensions in diabetic patients with manifest coronary artery disease. Circ Res 86: 998-1003.
10. Bai F, Rankinen T, Charbonneau C, Belsham DD, Rao DC, et al. (2004) Functional dimorphism of two hAgRP promoter SNPs in linkage disequilibrium. J Med Genet 41: 350-353.
11. Argyropoulos G, Rankinen T, Bai F, Rice T, Province MA, et al. (2003) The agouti-related protein and body fatness in humans. Int J Obes Relat Metab Disord 27: 276-280.
12. Rockman MV, Wray GA (2002) Abundant raw material for cis-regulatory evolution in humans. Mol Biol Evol 19: 1991-2004.
13. Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, et al. (2006) ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22: 637-640.
14. Buckland PR, Hoogendoorn B, Coleman SL, Guy CA, Smith SK, et al. (2005) Strong bias in the location of functional promoter polymorphisms. Hum Mutat 26: 214-223.
15. Pastinen T, Hudson TJ (2004) Cis-acting regulatory variation in the human genome. Science 306: 647-650.
16. Cavalieri D, Townsend JP, Hartl DL (2000) Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci U S A 97: 12369-12374.
17. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, et al. (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29: 389-395.
18. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
19. Cowles CR, Hirschhorn JN, Altshuler D, Lander ES (2002) Detection of regulatory variation in mouse genes. Nat Genet 32: 432-437.
20. Knight JC, Keating BJ, Rockett KA, Kwiatkowski DP (2003) In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat Genet 33: 469-475.
21. Pastinen T, Sladek R, Gurd S, Sammak A, Ge B, et al. (2004) A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics 16: 184-193.
22. Ronald J, Brem RB, Whittle J, Kruglyak L (2005) Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1: e25. doi:10.1371/journal. pgen.0010025
23. GuhaThakurta D, Xie T, Anand M, Edwards SW, Li G, et al. (2006) Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations. BMC Genomics 7: 235.
24. Stormo GD (2000) DNA binding sites: representation and discovery. Bioinformatics 16: 16-23.
25. Tronche F, Ringeisen F, Blumenfeld M, Yaniv M, Pontoglio M (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol 266: 231-245.
26. Fickett JW (1996) Quantitative discrimination of MEF2 sites. Mol Cell Biol 16: 437-441.
27. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26: 225-228.
28. Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, et al. (2003) Identification of conserved regulatory elements by comparative genome analysis. J Biol 2: 13.
29. Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5: 276-287.
30. Fields DS, He Y, Al-Uzri AY, Stormo GD (1997) Quantitative specificity of the Mnt repressor. J Mol Biol 271: 178-194.
31. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32 (Database issue): D91-D94.
32. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
33. Lenhard B, Hayes WS, Wasserman WW (2001) GeneLynx: a gene-centric portal to the human genome. Genome Res 11: 2151-2157.
34. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
35. Fredman D, Munns G, Rios D, Sjoholm F, Siegfried M, et al. (2004) HGVbase: a curated resource describing human DNA variation and phenotype relationships. Nucleic Acids Res 32 (Database issue): D516-D519.
36. Hudson TJ (2003) Wanted: regulatory SNPs. Nat Genet 33: 439-440.
37. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315: 233-237.
38. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
39. Uhlen M, Bjorling E, Agaton C, Szigyarto CA, Amini B, et al. (2005) A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 4: 1920-1932.
40. Wang X, Tomso DJ, Chorley BN, Cho HY, Cheung VG, et al. (2007) Identification of polymorphic antioxidant response elements in the human genome. Hum Mol Genet 16: 1188-1200.
41. Stepanova M, Tiazhelova T, Skoblov M, Baranova A (2006) Potential regulatory SNPs in promoters of human genes: a systematic approach. Mol Cell Probes 20: 348-358.
42. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31: 374-378.
43. Zhao T, Chang LW, McLeod HL, Stormo GD (2004) PromoLign: a database for upstream region analysis and SNPs. Hum Mutat 23: 534-539.
44. Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJ (2007) A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Comput Biol 3: e106. doi:10.1371/journal.pcbi.0030106
45. Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, et al. (2005) oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res 33: 3154-3164.
46. Cunniff NF, Morgan WD (1993) Analysis of heat shock element recognition by saturation mutagenesis of the human HSP70.1 gene promoter. J Biol Chem 268: 8317-8324.
47. Lenhard B, Wasserman WW (2002) TFBS: computational framework for transcription factor binding site analysis. Bioinformatics 18: 1135-1136.
48. Team RDC (2005) R: A language and environment for statistical computing; Computing RFfS, editor. Vienna, Austria.
49. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.
50. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res 31: 51-54.