Positive Selection in Alternatively Spliced Exons of Human Genes

American Journal of Human Genetics

Volumn 83, Issue 1, 2008, Pages 94-98

  Ramensky, Vasily E ^a   Nurtdinov, Ramil N ^b   Neverov, Alexei D ^c,d   Mironov, Andrei A ^b,c   Gelfand, Mikhail S ^b,e  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

^c STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

^d CENTRAL RESEARCH INSTITUTE OF EPIDEMIOLOGY   (Russian Federation)

^e INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; MESSENGER RNA;

ARTICLE; CHIMPANZEE; EVOLUTION; EXON; GENE SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; HUMAN; HUMAN GENETICS; NONHUMAN; PRIORITY JOURNAL; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CODON; DATABASES, FACTUAL; EXONS; EXPRESSED SEQUENCE TAGS; GENES; HUMANS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS); SEQUENCE HOMOLOGY, AMINO ACID;

PAN;

EID: 46149101497     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2008.05.017     Document Type: Article

References (30)

1. Graveley B.R. Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 17 (2001) 100-107
2. Lareau L.F., Green R.E., Bhatnagar R.S., and Brenner S.E. The evolving roles of alternative splicing. Curr. Opin. Struct. Biol. 14 (2004) 273-282
3. Mironov A.A., Fickett J.W., and Gelfand M.S. Frequent alternative splicing of human genes. Genome Res. 9 (1999) 1288-1293
4. Johnson J.M., Castle J., Garrett-Engele P., Kan Z., Loerch P.M., Armour C.D., Santos R., Schadt E.E., Stoughton R., and Shoemaker D.D. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302 (2003) 2141-2144
5. Kampa D., Cheng J., Kapranov P., Yamanaka M., Brubaker S., Cawley S., Drenkow J., Piccolboni A., Bekiranov S., Helt G., et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14 (2004) 331-342
6. Modrek B., and Lee C.J. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34 (2003) 177-180
7. Xing Y., and Lee C. Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet. 7 (2006) 499-509
8. Xing Y., and Lee C. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc. Natl. Acad. Sci. USA 102 (2005) 13526-13531
9. Ermakova E.O., Nurtdinov R.N., and Gelfand M.S. Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics 7 (2006) 84
10. Cusack B.P., and Wolfe K.H. Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Mol. Biol. Evol. 22 (2005) 2198-2208
11. Zhang X.H., and Chasin L.A. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc. Natl. Acad. Sci. USA 103 (2006) 13427-13432
12. Sabeti P.C., Schaffner S.F., Fry B., Lohmueller J., Varilly P., Shamovsky O., Palma A., Mikkelsen T.S., Altshuler D., and Lander E.S. Positive natural selection in the human lineage. Science 312 (2006) 1614-1620
13. Sabeti P.C., Varilly P., Fry B., Lohmueller J., Hostetter E., Cotsapas C., Xie X., Byrne E.H., McCarroll S.A., Gaudet R., et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449 (2007) 913-918
14. McDonald J.H., and Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351 (1991) 652-654
15. Fay J.C., Wyckoff G.J., and Wu C.I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415 (2002) 1024-1026
16. Bustamante C.D., Fledel-Alon A., Williamson S., Nielsen R., Hubisz M.T., Glanowski S., Tanenbaum D.M., White T.J., Sninsky J.J., Hernandez R.D., et al. Natural selection on protein-coding genes in the human genome. Nature 437 (2005) 1153-1157
17. Nurtdinov R.N., Neverov A.D., Mal'ko D.B., Kosmodem'ianskii I.A., Ermakova E.O., Ramenskii V.E., Mironov A.A., and Gel'fand M.S. Biofizika 51 (2006) 589-592
18. Neverov A.D., Artamonova I.I., Nurtdinov R.N., Frishman D., Gelfand M.S., and Mironov A.A. Alternative splicing and protein function. BMC Bioinformatics 7 (2005) 266
19. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., and Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29 (2001) 308-311
20. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., and Haussler D. The human genome browser at UCSC. Genome Res. 12 (2002) 996-1006
21. Kondrashov F.A., Ogurtsov A.Y., and Kondrashov A.S. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. J. Theor. Biol. 240 (2006) 616-626
22. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.J., Makhijani V., Roth G.T., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452 (2008) 872-876
23. Smith N.G., and Eyre-Walker A. Adaptive protein evolution in Drosophila. Nature 415 (2002) 1022-1024
24. Lev-Maor G., Goren A., Sela N., Kim E., Keren H., Doron-Faigenboim A., Leibman-Barak S., Pupko T., and Ast G. The "alternative" choice of constitutive exons throughout evolution. PLoS Genet. 3 (2007) e203
25. Carlini D.B., and Genut J.E. Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J. Mol. Evol. 62 (2006) 89-98
26. Fairbrother W.G., Holste D., Burge C.B., and Sharp P.A. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol. 2 (2004) E268
27. Orban T.I., and Olah E. Purifying selection on silent sites-a constraint from splicing regulation?. Trends Genet. 5 (2001) 252-253
28. Parmley J.L., Chamary J.V., and Hurst L.D. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 23 (2006) 301-309
29. Alekseyenko A.V., Kim N., and Lee C.J. Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA 13 (2007) 661-670
30. Sorek R., Shamir R., and Ast G. How prevalent is functional alternative splicing in the human genome?. Trends Genet. 20 (2004) 68-71