A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Churbanov, Alexander ^a   Vořechovský, Igor ^b   Hicks, Chindo ^c  

^a NEW MEXICO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^c LOYOLA UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTISM SPECTRUM DISORDERS; BREAST CANCER; CIS-ACTING ELEMENT; CIS-REGULATORY ELEMENTS; GENETIC DISORDERS; GENETIC VARIANTS; HEREDITARY DISORDERS; POLYMORPHIC VARIANT;

DISEASES; TOOLS;

FORECASTING;

ISOPROTEIN;

ARTICLE; BREAST TUMOR; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENETICS; HUMAN; HUMAN GENOME; METHODOLOGY; RNA SPLICING;

BREAST NEOPLASMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME, HUMAN; HUMANS; PROTEIN ISOFORMS; RNA SPLICING;

EID: 77249135158     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-22     Document Type: Article

References (57)

1. Mount SM. Genomic sequence, splicing, and gene annotation. Am J Hum Genet 2000, 67(4):788-792. 10.1086/303098, 1287883, 10986039.
2. Lim LP, Burge CB. A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci USA 2001, 98(20):11193-11198. 10.1073/pnas.201407298, 58706, 11572975.
3. Wang Z, Burge CB. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 2008, 14(5):802-813. 10.1261/rna.876308, 2327353, 18369186.
4. Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002, 3(4):285-298. 10.1038/nrg775, 11967553.
5. Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R. Are splicing mutations the most frequent cause of hereditary disease?. FEBS Lett 2005, 579(9):1900-1903. 10.1016/j.febslet.2005.02.047, 15792793.
6. Stenson PD, Ball E, Howells K, Phillips A, Mort M, Cooper DN. Human Gene Mutation Database: towards a comprehensive central mutation database. J Med Genet 2008, 45(2):124-126. 10.1136/jmg.2007.055210, 18245393.
7. Buratti E, Chivers M, Kralovicova J, Romano M, Baralle M, Krainer AR, Vorechovsky I. Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 2007, 35(13):4250-4263. 10.1093/nar/gkm402, 1934990, 17576681.
8. Vorechovsky I. Aberrant 3' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Res 2006, 34(16):4630-4641. 10.1093/nar/gkl535, 1636351, 16963498.
9. Garcia-Blanco MA, Baraniak AP, Lasda EL. Alternative splicing in disease and therapy. Nat Biotechnol 2004, 22(5):535-546. 10.1038/nbt964, 15122293.
10. Hua Y, Vickers TA, Okunola HL, Bennett CF, Krainer AR. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet 2008, 82(4):834-848. 10.1016/j.ajhg.2008.01.014, 2427210, 18371932.
11. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456(7221):470-476. 10.1038/nature07509, 2593745, 18978772.
12. Burset M, Seledtsov IA, Solovyev VV. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res 2000, 28(21):4364-4375. 10.1093/nar/28.21.4364, 113136, 11058137.
13. Thanaraj TA, Clark F. Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. Nucleic Acids Res 2001, 29(12):2581-2593. 10.1093/nar/29.12.2581, 55748, 11410667.
14. Churbanov A, Winters-Hilt S, Koonin EV, Rogozin IB. Accumulation of GC donor splice signals in mammals. Biol Direct 2008, 3:30. 10.1186/1745-6150-3-30, 2490688, 18613975.
15. Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res 2006, 34(14):3955-3967. 10.1093/nar/gkl556, 1557818, 16914448.
16. Sparks ME, Brendel V. Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics 2005, 21(Suppl 3):iii20-30. 10.1093/bioinformatics/bti1205, 16306388.
17. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouze P, Brunak S. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res 1996, 24(17):3439-3452. 10.1093/nar/24.17.3439, 146109, 8811101.
18. Sun H, Chasin LA. Multiple splicing defects in an intronic false exon. Mol Cell Biol 2000, 20(17):6414-6425. 10.1128/MCB.20.17.6414-6425.2000, 86117, 10938119.
19. Fickett JW, Tung CS. Assessment of protein coding measures. Nucleic Acids Res 1992, 20(24):6441-6450. 10.1093/nar/20.24.6441, 334555, 1480466.
20. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268(1):78-94. 10.1006/jmbi.1997.0951, 9149143.
21. Krogh A. Two methods for improving performance of an HMM and their application for gene finding. Proc Int Conf Intell Syst Mol Biol 1997, 5:179-186.
22. Krogh A. Gene finding: putting the parts together. Guide to human genome computing 1998, 261-274. Academic Press, San Diego, CA, Bishop MJ, 2.
23. Churbanov A, Rogozin IB, Deogun JS, Ali H. Method of predicting splice sites based on signal interactions. Biol Direct 2006, 1:10. 10.1186/1745-6150-1-10, 1526722, 16584568.
24. Eden E, Brunak S. Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA. Nucleic Acids Res 2004, 32(3):1131-1142. 10.1093/nar/gkh273, 373407, 14960723.
25. Rogozin IB, Milanesi L. Analysis of donor splice sites in different eukaryotic organisms. J Mol Evol 1997, 45(1):50-59. 10.1007/PL00006200, 9211734.
26. Mache N, Levi P. GENIO- A Non-Redundant Eukaryotic Gene Database of Annotated Sites and Sequences. RECOMB 1998,
27. Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004, 11(2-3):377-394. 10.1089/1066527041410418, 15285897.
28. Eng L, Coutinho G, Nahas S, Yeo G, Tanouye R, Babaei M, Dork T, Burge C, Gatti RA. Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths. Hum Mutat 2004, 23(1):67-76. 10.1002/humu.10295, 14695534.
29. Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB. Systematic identification and analysis of exonic splicing silencers. Cell 2004, 119(6):831-845. 10.1016/j.cell.2004.11.010, 15607979.
30. Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science 2002, 297(5583):1007-1013. 10.1126/science.1073774, 12114529.
31. Kralovicova J, Vorechovsky I. Position-dependent repression and promotion of DQB1 intron 3 splicing by GGGG motifs. J Immunol 2006, 176(4):2381-2388.
32. Divina P, Kvitkovicova A, Buratti E, Vorechovsky I. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet 2009, 17(6):759-765. 10.1038/ejhg.2008.257, 19142208.
33. Kralovicova J, Vorechovsky I. Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition. Nucleic Acids Res 2007, 35(19):6399-6413. 10.1093/nar/gkm680, 2095810, 17881373.
34. Churbanov A. Contemporary progress in gene structure prediction. Current genomics 2006, 7(5):283-292.
35. Yeo G, Hoon S, Venkatesh B, Burge CB. Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci USA 2004, 101(44):15700-15705. 10.1073/pnas.0404901101, 524216, 15505203.
36. Abril JF, Castelo R, Guigo R. Comparison of splice sites in mammals and chicken. Genome Res 2005, 15(1):111-119. 10.1101/gr.3108805, 540285, 15590946.
37. Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res 2004, (32 Web Server):W187-190. 10.1093/nar/gkh393, 441531, 15215377.
38. Minovitsky S, Gee SL, Schokrpur S, Dubchak I, Conboy JG. The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. Nucleic Acids Res 2005, 33(2):714-724. 10.1093/nar/gki210, 548355, 15691898.
39. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science 2004, 304(5675):1321-1325. 10.1126/science.1098119, 15131266.
40. Churbanov A, Vorechovsky I, Hicks C. Computational prediction of splicing regulatory elements shared by Tetrapoda organisms. BMC Genomics 2009, 10:508. 10.1186/1471-2164-10-508, 2777938, 19889216.
41. Berget SM. Exon recognition in vertebrate splicing. J Biol Chem 1995, 270(6):2411-2414.
42. Rebbeck TR, Ambrosone CB, Bell DA, Chanock SJ, Hayes RB, Kadlubar FF, Thomas DC. SNPs, haplotypes, and cancer: applications in molecular epidemiology. Cancer Epidemiol Biomarkers Prev 2004, 13(5):681-687.
43. Zhang C, Li WH, Krainer AR, Zhang MQ. RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci USA 2008, 105(15):5797-5802. 10.1073/pnas.0801692105, 2311341, 18391195.
44. Zhang MQ. Statistical features of human exons and their flanking regions. Hum Mol Genet 1998, 7(5):919-932. 10.1093/hmg/7.5.919, 9536098.
45. Hwang DY, Cohen JB. U1 small nuclear RNA-promoted exon selection requires a minimal distance between the position of U1 binding and the 3' splice site across the exon. Mol Cell Biol 1997, 17(12):7099-7107. 232566, 9372941.
46. Felsenstein J. Inferring phylogenies. 2004, Sinauer Associates, Inc, Sunderland, Massachusetts.
47. Zheng ZM, He P, Baker CC. Selection of the bovine papillomavirus type 1 nucleotide 3225 3' splice site is regulated through an exonic splicing enhancer and its juxtaposed exonic splicing suppressor. J Virol 1996, 70(7):4691-4699. 190405, 8676495.
48. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 2007, 39(7):870-874. 10.1038/ng2075, 17529973.
49. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007, 447(7148):1087-1093. 10.1038/nature05887, 2714974, 17529967.
50. Listgarten J, Damaraju S, Poulin B, Cook L, Dufour J, Driga A, Mackey J, Wishart D, Greiner R, Zanke B. Predictive models for breast cancer susceptibility from multiple single nucleotide polymorphisms. Clin Cancer Res 2004, 10(8):2725-2737. 10.1158/1078-0432.CCR-1115-03, 15102677.
51. Commonly studied single-nucleotide polymorphisms and breast cancer: results from the Breast Cancer Association Consortium. J Natl Cancer Inst 2006, 98(19):1382-1396.
52. Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, Masson G, Jakobsdottir M, Thorlacius S, Helgason A, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 2007, 39(7):865-869. 10.1038/ng2064, 17529974.
53. Benusiglio PR, Lesueur F, Luccarini C, Conroy DM, Shah M, Easton DF, Day NE, Dunning AM, Pharoah PD, Ponder BA. Common ERBB2 polymorphisms and risk of breast cancer in a white British population: a case-control study. Breast Cancer Res 2005, 7(2):R204-209. 10.1186/bcr982, 1064135, 15743501.
54. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
55. Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
56. Cogan JD, Pauciulo MW, Batchman AP, Prince MA, Robbins IM, Hedges LK, Stanton KC, Wheeler LA, Phillips JA, Loyd JE, et al. High frequency of BMPR2 exonic deletions/duplications in familial pulmonary arterial hypertension. Am J Respir Crit Care Med 2006, 174(5):590-598. 10.1164/rccm.200602-165OC, 2648061, 16728714.
57. Parkinson GN. Fundamentals of Quadruplex Structures. Quadruplex Nucleic Acids 2006, 1-30. Cambridge: RSC, Neidle S, Balasubramanian S.