Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events

PLoS Computational Biology

Volumn 4, Issue 1, 2008, Pages 0004-0013

  Holste, Dirk ^a   Ohler, Uwe ^b  

^a INSTITUTE OF MOLECULAR BIOTECHNOLOGY   (Austria)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS;

ALTERNATIVE SPLICING; REGULATORY MOTIFS; RNA SPLICING;

RNA;

MESSENGER RNA PRECURSOR; RIBONUCLEOPROTEIN; SMALL NUCLEAR RNA; MESSENGER RNA;

AB INITIO CALCULATION; ALTERNATIVE RNA SPLICING; EXON; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; INTRON; MAMMAL; MATHEMATICAL COMPUTING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN MOTIF; REVIEW; RNA PROCESSING; RNA SPLICING; SPLICEOSOME; ALGORITHM; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENETICS; METHODOLOGY; REGULATORY RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SYSTEM ANALYSIS; UNTRANSLATED REGION;

ALGORITHMS; MODELS, GENETIC; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA SPLICE SITES; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; SYSTEMS INTEGRATION; UNTRANSLATED REGIONS;

EID: 38949107416     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0040021     Document Type: Review

References (73)

1. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416: 499-506.
2. Burge C, Tuschl T, Sharp P (1999) Splicing of precursors to mRNAs by the spliceosomes. In: Gesteland R, Cech T, Atkins J, editors. The RNA world. 2nd edition. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. pp. 525-560.
3. Lopez AJ (1998) Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation. Annu Rev Genet 32: 279-305.
4. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72: 291-336.
5. Jurica MS, Moore MJ (2003) Pre-mRNA splicing: Awash in a sea of proteins. Mol Cell 12: 5-14.
6. Nilsen TW (2003) The spliceosome: The most complex macromolecular machine in the cell? Bioessays 25: 1147-1149.
7. Graveley BR (2001) Alternative splicing: Increasing diversity in the proteomic world. Trends Genet 17: 100-107.
8. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
9. Modrek B, Lee CJ (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet 34: 177-180.
10. Holste D, Huo G, Tung V, Burge CB (2006) HOLLYWOOD: A comparative relational database of alternative splicing. Nucleic Acids Res 34: D56-D62.
11. Faustino NA, Cooper TA (2003) Pre-mRNA splicing and human disease. Genes Dev 17: 419-437.
12. Lejeune F, Maquat LE (2005) Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr Opin Cell Biol 17: 309-315.
13. Lewis BP, Green RE, Brenner SE (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A 100: 189-192.
14. Pan Q, Saltzman AL, Kim YK, Misquitta C, Shai O, et al. (2006) Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev 20: 153-158.
15. Lareau LF, Green RE, Bhatnagar RS, Brenner SE (2004) The evolving roles of alternative splicing. Curr Opin Struct Biol 14: 273-282.
16. Lee C, Wang Q (2005) Bioinformatics analysis of alternative splicing. Brief Bioinform 6: 23-33.
17. Cartegni L, Chew SL, Krainer AR (2002) Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat Rev Genet 3: 285-298.
18. Matlin AJ, Clark F, Smith CW (2005) Understanding alternative splicing: Towards a cellular code. Nat Rev Mol Cell Biol 6: 386-398.
19. Ast G (2004) How did alternative splicing evolve? Nat Rev Genetics 5: 773-782.
20. Xing Y, Lee C (2006) Alternative splicing and RNA selection pressure - Evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7: 499-509.
21. Kan Z, States D, Gish W (2002) Selecting for functional alternative splices in ESTs. Genome Res 12: 1837-1845.
22. Yeo G, Holste D, Kreiman G, Burge CB (2004) Variation in alternative splicing across human tissues. Genome Biol 5: R74.
23. Kim E, Magen A, Ast G (2007) Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 35: 125-131.
24. Brett D, Pospisil H, Valcarcel J, Reich J, Bork P (2002) Alternative splicing and genome complexity. Nat Genet 30: 29-30.
25. Lim LP, Burge CB (2001) A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A 98: 11193-11198.
26. Irimia M, Penny D, Roy SW (2007) Coevolution of genomic intron number and splice sites. Trends Genet 23: 321-325.
27. Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, et al. (2004) Systematic identification and analysis of exonic splicing silencers. Cell 119: 831-845.
28. Fairbrother WG, Yeh RF, Sharp PA, Burge CB (2002) Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
29. Zheng CL, Fu XD, Gribskov M (2005) Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. Rna 11: 1777-1787.
30. Wang J, Smith PJ, Krainer AR, Zhang MQ (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res 33: 5053-5062.
31. Zheng ZM (2004) Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. J Biomed Sci 11: 278-294.
32. Ladd AN, Cooper TA (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol 3: reviews0008.
33. Jensen KB, Dredge BK, Stefani G, Zhong R, Buckanovich RJ, et al. (2000) Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability. Neuron 25: 359-371.
34. Grabowski PJ (2000) Genetic evidence for a Nova regulator of alternative splicing in the brain. Neuron 25: 254-256.
35. Rahman L, Bliskovski V, Reinhold W, Zajac-Kaye M (2002) Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles. Genomics 80: 245-249.
36. Jin Y, Suzuki H, Maegawa S, Endo H, Sugano S, et al. (2003) A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J 22: 905-912.
37. Nakahata S, Kawamoto S (2005) Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities. Nucleic Acids Res 33: 2078-2089.
38. Brudno M, Gelfand MS, Spengler S, Zorn M, Dubchak I, et al. (2001) Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing. Nucleic Acids Res 29: 2338-2348.
39. Liu HX, Zhang M, Krainer AR (1998) Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev 12: 1998-2012.
40. Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR (2003) ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res 31: 3568-3571.
41. Fairbrother WG, Holste D, Burge CB, Sharp PA (2004) Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2: e268. doi:10.1371/journal.pbio.0020268
42. Zhang XH, Chasin LA (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 18: 1241-1250.
43. Goren A, Ram O, Amit M, Keren H, Lev-Maor G, et al. (2006) Comparative analysis identifies exonic splicing regulatory sequences - The complex definition of enhancers and silencers. Mol Cell 22: 769-781.
44. Yeo GW, Nostrand EL, Liang TY (2007) Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet 3: e85. doi:10.1371/journal.pgen.0030085
45. Kabat JL, Barberan-Soler S, McKenna P, Clawson H, Farrer T, et al. (2006) Intronic alternative splicing regulators identified by comparative genomics in nematodes. PLoS Comput Biol 2: e86. doi:10.1371/journal.pcbi.0020086
46. Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, et al. (2006) Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet 2: e191. doi:10.1371/journal.pgen.0020191
47. Baek D, Green P (2005) Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci U S A 102: 12813-12818.
48. Wang W, Zheng H, Yang S, Yu H, Li J, et al. (2005) Origin and evolution of new exons in rodents. Genome Res 15: 1258-1264.
49. Hong X, Scofield DG, Lynch M (2006) Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol 23: 2392-2404.
50. Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB (2005) Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A 102: 2850-2855.
51. Nurtdinov RN, Artamonova II, Mironov AA, Gelfand MS (2003) Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet 12: 1313-1320.
52. Thanaraj TA, Clark F, Muilu J (2003) Conservation of human alternative splice events in mouse. Nucleic Acids Res 31: 2544-2552.
53. Sorek R, Ast G (2003) Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res 13: 1631-1637.
54. Ratsch G, Sonnenburg S, Scholkopf B (2005) RASE: recognition of alternatively spliced exons in C. elegans. Bioinformatics 21: i369-377.
55. Philipps DL, Park JW, Graveley BR (2004) A computational and experimental approach toward a priori identification of alternatively spliced exons. Rna 10: 1838-1844.
56. Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, et al. (2004) A non-EST-based method for exon-skipping prediction. Genome Res 14: 1617-1623.
57. Dror G, Sorek R, Shamir R (2005) Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics 21: 897-901.
58. Sharan R, Myers EW (2005) A motif-based framework for recognizing sequence families. Bioinformatics 21: i387-393.
59. Ohler U, Shomron N, Burge CB (2005) Recognition of unknown conserved alternatively spliced exons. PLoS Comput Biol 1: 113-122.
60. Durbin R, Eddy SR, Krogh A, Mitchison G (1998) Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge (United Kingdom): Cambridge University Press.
61. Allen JE, Salzberg SL (2006) A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms Mol Biol 1: 14.
62. Letunic I, Copley RR, Bork P (2002) Common exon duplication in animals and its role in alternative splicing. Hum Mol Genet 11: 1561-1567.
63. Hiller M, Huse K, Platzer M, Backofen R (2005) Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res 33: 5611-5621.
64. Leparc GG, Mitra RD (2007) Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Res 35: 3192-3202.
65. Sorek R, Dror G, Shamir R (2006) Assessing the number of ancestral alternatively spliced exons in the human genome. BMC Genomics 7: 273.
66. Cawley SL, Pachter L (2003) HMM sampling and applications to gene finding and alternative splicing. Bioinformatics 19: II36-II41.
67. Flicek P, Brent MR (2006) Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. Genome Biol 7: S8 1-9.
68. Ratsch G, Sonnenburg S, Srinivasan J, Witte H, Muller KR, et al. (2007) Improving the Caenorhabditis elegans genome annotation using machine learning. PLoS Comput Biol 3: e20. doi:10.1371/journal.pcbi.0030020
69. Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O, et al. (2000) An alternative-exon database and its statistical analysis. DNA Cell Biol 19: 739-756.
70. Shah PK, Jensen LJ, Boue S, Bork P (2005) Extraction of transcript diversity from scientific literature. PLoS Comput Biol 1: e10. doi:10.1371/journal.pcbi.0010010
71. Spellman R, Rideau A, Matlin A, Gooding C, Robinson F, et al. (2005) Regulation of alternative splicing by PTB and associated factors. Biochem Soc Trans 33: 457-460.
72. Wollerton MC, Gooding C, Wagner EJ, Garcia-Blanco MA, Smith CW (2004) Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol Cell 13: 91-100.
73. Graveley BR (2005) Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 123: 65-73.