Alternatively and constitutively spliced exons are subject to different evolutionary forces

Molecular Biology and Evolution

Volumn 23, Issue 3, 2006, Pages 675-682

  Chen, Feng Chi ^a   Wang, Sheng Shun ^b   Chen, Chuang Jong ^a   Li, Wen Hsiung ^a,c   Chuang, Trees Juen ^a  

^a GENOMICS RESEARCH CENTER   (Taiwan)

^b INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

Alternatively spliced exons; Comparative genomics; Constitutively spliced exons; Selective constraint; Synonymous nonsynonymous substitution

Indexed keywords

AMINO ACID; DINUCLEOTIDE;

ALTERNATIVE RNA SPLICING; AMINO ACID BLOOD LEVEL; ARTICLE; CONTROLLED STUDY; EXON; GENE FUNCTION; GENE STRUCTURE; HUMAN; INTRON; MAJOR CLINICAL STUDY; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MOUSE; NEUTRAL GENE THEORY; NONHUMAN; RAT;

ANIMALS; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; EXONS; HUMANS; INTRONS; MICE; RNA SPLICING;

MAMMALIA;

EID: 33244483948     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj081     Document Type: Article

References (67)

1. Baek, D., and P. Green. 2005. Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc. Natl. Acad. Sci. USA 102:12813-12818.
2. Boue, S., I. Letunic, and P. Bork. 2003. Alternative splicing and evolution. Bioessays 25:1031-1034.
3. Cargill, M., D. Altshuler, J. Ireland et al. (18 co-authors). 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22:231-238.
4. Castresana, J. 2002. Estimation of genetic distances from human and mouse introns. Genome Biol. 3:RESEARCH0028.
5. Chuang, T. J., W. C. Lin, H. C. Lee, C. W. Wang, K. L. Hsiao, Z. H. Wang, D. Shieh, S. C. Lin, and L. Y. Ch'ang. 2003. A complexity reduction algorithm for analysis and annotation of large genomic sequences. Genome Res. 13:313-322.
6. Cline, M. S., R. Shigeta, R. L. Wheeler, M. A. Siani-Rose, D. Kulp, and A. E. Loraine. 2004. The effects of alternative splicing on transmembrane proteins in the mouse genome. Pp. 17-28 in Altman R.B., A.K. Dunker, L. Hunter, T.A. Jung, and T.E. Klein, eds. Biocomputing 2004. Proceedings of the Pacific Symposium; 2004 Jan 6-10; Big Island, Hawaii. World Scientific, Hackensack, N.J.
7. Cusack, B. P., and K. H. Wolfe. 2005. Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Mol. Biol. Evol. 22:2198-2208.
8. Fairbrother, W. G., D. Holste, C. B. Burge, and P. A. Sharp. 2004a. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2:E268.
9. Fairbrother, W. G., G. W. Yeo, R. Yeh, P. Goldstein, M. Mawson, P. A. Sharp, and C. B. Burge. 2004b. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res. 32:W187-W190.
10. Filip, L. C., and N. I. Mundy. 2004. Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates. Mol. Biol. Evol. 21:1504-1511.
11. Garcia-Blanco, M. A., A. P. Baraniak, and E. L. Lasda. 2004. Alternative splicing in disease and therapy. Nat. Biotechnol. 22:535-546.
12. Gibbs, R. A., G. M. Weinstock, M. L. Metzker et al. (229 co-authors). 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.
13. Gilbert, W. 1978. Why genes in pieces? Nature 271:501.
14. Graur, D. 1985. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22:53-62.
15. Halushka, M. K., J. B. Fan, K. Bentley, L. Hsie, N. Shen, A. Weder, R. Cooper, R. Lipshutz, and A. Chakravarti. 1999. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22:239-247.
16. Hanke, J., D. Brett, I. Zastrow, A. Aydin, S. Delbruck, G. Lehmann, F. Luft, J. Reich, and P. Bork. 1999. Alternative splicing of human genes: more the rule than the exception? Trends Genet. 15:389-390.
17. Hillier, L. W., W. Miller, E. Birney et al (175 co-authors). 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
18. Hurst, L. D., and C. Pal. 2001. Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet. 17:62-65.
19. Iida, K., and H. Akashi. 2000. A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261:93-105.
20. Itoh, H., T. Washio, and M. Tomita. 2004. Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA 10:1005-1018.
21. Kan, Z., E. C. Rouchka, W. R. Gish, and D. J. States. 2001. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 11:889-900.
22. Kan, Z., D. States, and W. Gish. 2002. Selecting for functional alternative splices in ESTs. Genome Res. 12:1837-1845.
23. Keightley, P. D., and D. J. Gaffney. 2003. Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc. Natl. Acad. Sci. USA 100:13402-13406.
24. Kondrashov, F. A., and E. V. Koonin. 2003. Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet. 19:115-119.
25. Kriventseva, E. V., I. Koch, R. Apweiler, M. Vingron, P. Bork, M. S. Gelfand, and S. Sunyaev. 2003. Increase of functional diversity by alternative splicing. Trends Genet. 19:124-128.
26. Lee, C., L. Atanelov, B. Modrek, and Y. Xing. 2003. ASAP: the alternative splicing annotation project. Nucleic Acids Res. 31:101-105.
27. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
28. Li, W. H., C. I. Wu, and C. C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
29. Linding, R., R. B. Russell, V. Neduva, and T. J. Gibson. 2003. GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31:3701-3708.
30. Mironov, A. A., J. W. Fickett, and M. S. Gelfand. 1999. Frequent alternative splicing of human genes. Genome Res. 9:1288-1293.
31. Modrek, B., and C. Lee. 2002. A genomic view of alternative splicing. Nat. Genet. 30:13-19.
32. Modrek, B., and C. J. Lee. 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.
33. Modrek, B., A. Resch, C. Grasso, and C. Lee. 2001. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29:2850-2859.
34. Moriyama, E. N., and J. R. Powell. 1996. Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13:261-277.
35. Mulder, N. J., R. Apweiler, T. K. Attwood et al. (40 co-authors). 2005. InterPro, progress and status in 2005. Nucleic Acids Res. 33:D201-D205.
36. Nekrutenko, A., W. Y. Chung, and W. H. Li. 2003. An evolutionary approach reveals a high protein-coding capacity of the human genome. Trends Genet. 19:306-310.
37. Nobrega, M. A., I. Ovcharenko, V. Afzal, and E. M. Rubin. 2003. Scanning human gene deserts for long-range enhancers. Science 302:413.
38. Nobrega, M. A., Y. Zhu, I. Plajzer-Frick, V. Afzal, and E. M. Rubin. 2004. Megabase deletions of gene deserts result in viable mice. Nature 431:988-993.
39. Nurtdinov, R. N., I. I. Artamonova, A. A. Mironov, and M. S. Gelfand. 2003. Low conservation of alternative splicing patterns in the human and mouse genomes. Hum. Mol. Genet. 12:1313-1320.
40. Orban, T. I., and E. Olah. 2003. Emerging roles of BRCA1 alternative splicing. Mol. Pathol. 56:191-197.
41. Ovcharenko, I., G. G. Loots, M. A. Nobrega, R. C. Hardison, W. Miller, and L. Stubbs. 2005. Evolution and functional classification of vertebrate gene deserts. Genome Res. 15:137-145.
42. Pagani, F., M. Raponi, and F. E. Baralle. 2005. Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc. Natl. Acad. Sci. USA 102:6368-6372.
43. Philipps, D. L., J. W. Park, and B. R. Graveley. 2004. A computational and experimental approach toward a priori identification of alternatively spliced exons. RNA 10:1838-1844.
44. Quevillon, E., V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33:W116-W120.
45. Rastegar, M., L. Kobrossy, E. N. Kovacs, I. Rambaldi, and M. Featherstone. 2004. Sequential histone modifications at Hoxd4 regulatory regions distinguish anterior from posterior embryonic compartments. Mol. Cell Biol. 24:8090-8103.
46. Resch, A., Y. Xing, A. Alekseyenko, B. Modrek, and C. Lee. 2004. Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res. 32:1261-1269.
47. Rossi, E. L. 2004. Stress-induced alternative gene splicing in mind-body medicine. Adv. Mind Body Med. 20:12-19.
48. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
49. Sazani, P., and R. Kole. 2003. Therapeutic potential of antisense oligonucleotides as modulators of alternative splicing. J. Clin. Investig. 112:481-486.
50. Sorek, R., and G. Ast. 2003. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13:1631-1637.
51. Sorek, R., R. Shemesh, Y. Cohen, O. Basechess, G. Ast, and R. Shamir. 2004. A non-EST-based method for exon-skipping prediction. Genome Res. 14:1617-1623.
52. Stamm, S., S. Ben-Ari, I. Rafalska, Y. Tang, Z. Zhang, D. Toiber, T. A. Thanaraj, and H. Soreq. 2005. Function of alternative splicing. Gene 344:1-20.
53. Subramanian, S., and S. Kumar. 2003. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13:838-844.
54. Sugnet, C. W., W. J. Kent, M. Ares Jr., and D. Haussler. 2004. Transcriptome and genome conservation of alternative splicing events in humans and mice. Pp. 66-77 in Altman R.B., A.K. Dunker, L. Hunter, T.A. Jung, and T.E. Klein, eds. Biocomputing 2004. Proceedings of the Pacific Symposium; 2004 Jan 6-10; Big Island, Hawaii. World Scientific, Hackensack, N.J.
55. Venables, J. P. 2004. Aberrant and alternative splicing in cancer. Cancer Res. 64:7647-7654.
56. Wachtel, C., B. Li, J. Sperling, and R. Sperling. 2004. Stop codonmediated suppression of splicing is a novel nuclear scanning mechanism not affected by elements of protein synthesis and NMD. RNA 10:1740-1750.
57. Wang, Z., M. E. Rolish, G. Yeo, V. Tung, M. Mawson, and C. B. Burge. 2004. Systematic identification and analysis of exonic splicing silencers. Cell 119:831-845.
58. Waterston, R. H., K. Lindblad-Toh, E. Birney et al. (222 co-authors). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
59. Wu, J. Y., H. Tang, and N. Havlioglu. 2003. Alternative pre-mRNA splicing and regulation of programmed cell death. Prog. Mol. Subcell. Biol. 31:153-185.
60. Xing, Y., and C. Lee. 2005a. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc. Natl. Acad. Sci. USA 102:13526-13531.
61. _. 2005b. Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics 21:3701-3703.
62. Xing, Y., and C. J. Lee. 2004. Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends Genet. 20:472-475.
63. Xing, Y., Q. Xu, and C. Lee. 2003. Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Lett. 555:572-578.
64. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
65. Yang, Z., and R. Nielsen. 2000. Estimating synonymous and non-synonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43.
66. Yeo, G. W., E. Van Nostrand, D. Holste, T. Poggio, and C. B. Burge. 2005. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102:2850-2855.
67. Zwick, M. E., D. J. Cutler, and A. Chakravarti. 2000. Patterns of genetic variation in Mendelian and complex traits. Annu. Rev. Genomics Hum. Genet. 1:387-407.