Genome-wide evidence for selection acting on single amino acid repeats

Genome Research

Volumn 20, Issue 6, 2010, Pages 755-760

  Haerty, Wilfried ^a   Golding, G Brian ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; MESSENGER RNA;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; CODON; DROSOPHILA MELANOGASTER; EUKARYOTE; EXON; GENOME; HUMAN; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL;

ALTERNATIVE SPLICING; AMINO ACIDS; ANIMALS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EXONS; HUMANS; MICE; REPETITIVE SEQUENCES, AMINO ACID; ZEBRAFISH;

EUKARYOTA;

EID: 77952988983     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.101246.109     Document Type: Article

References (48)

1. Al-Shahrour F, Minguez P, Tarraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J, et al. 2006. BABELOMICS: A systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 34: W472-W476. (Pubitemid 44529816)
2. Alba MM, Guigo R. 2004. Comparative analysis of amino acid repeats in rodents and humans. Genome Res 14: 549-554. (Pubitemid 38500225)
3. Alba MM, Santibanez-Koref MF, Hancock JM. 1999a. Amino acid reiterations in yeast are overrepresented in particular classes of proteins and show evidence of a slippage-like mutational process. J Mol Evol 49: 789-797.
4. Alba MM, Santibanez-Koref MF, Hancock JM. 1999b. Conservation of polyglutamine tract size between mice and humans depends on codon interruption. Mol Biol Evol 16: 1641-1644.
5. Alba MM, Santibanez-Koref MF, Hancock JM. 2001. The comparative genomics of polyglutamine repeats: Extreme differences in the codon organization of repeat-encoding regions between mammals and Drosophila. J Mol Evol 52: 249-259. (Pubitemid 32299607)
6. Ast G. 2004. How did alternative splicing evolve? Nat Rev Genet 5: 773-782.
7. Bannen RM, Bingman CA, Phillips GN Jr. 2007. Effect of low-complexity regions on protein structure determination. J Struct Funct Genomics 8: 217-226.
8. Blencowe BJ. 2006. Alternative splicing: New insights from global analyses. Cell 126: 37-47.
9. Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, Oldfield CJ, Williams CJ, Dunker AK. 2002. Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 55: 104-110. (Pubitemid 34634364)
10. Chen FC, Wang SS, Chen CJ, Li WH, Chuang TJ. 2006. Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol 23: 675-682.
11. Dieringer D, Schlotterer C. 2003. Two distinct modes of microsatellite mutation processes: Evidence from the complete genomic sequences of nine species. Genome Res 13: 2242-2251. (Pubitemid 37265989)
12. Ermakova EO, Nurtdinov RN, Gelfand MS. 2006. Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics 7: 84. doi: 10.1186/1471-2164-7-84.
13. Faux NG, Bottomley SP, Lesk AM, Irving JA, Morrison JR, de la Banda MG, Whisstock JC. 2005. Functional insights from the distribution and role of homopeptide repeat-containing proteins. Genome Res 15: 537-551.
14. Felsenstein J. 1989. PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics 5: 164-166.
15. Fondon JW III, Garner HR. 2004. Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci 101: 18058-18063.
16. Golding GB. 1999. Simple sequence is abundant in eukaryotic proteins. Protein Sci 8: 1358-1361.
17. Haerty W, Golding B. 2009. Similar selective factors affect both between-gene and between-exon divergence in Drosophila. Mol Biol Evol 26: 859-866.
18. Hancock JM, Simon M. 2005. Simple sequence repeats in proteins and their significance for network evolution. Gene 345: 113-118. (Pubitemid 40208507)
19. Hancock JM, Worthey EA, Santibanez-Koref MF. 2001. A role for selection in regulating the evolutionary emergence of disease-causing and other coding CAG repeats in humans and mice. Mol Biol Evol 18: 1014-1023.
20. Huntley MA, Clark AG. 2007. Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species. Mol Biol Evol 24: 2598-2609.
21. Huntley M, Golding GB. 2000. Evolution of simple sequence in proteins. J Mol Evol 51: 131-140.
22. Huntley MA, Golding GB. 2002. Simple sequences are rare in the Protein Data Bank. Proteins 48: 134-140.
23. Huntley MA, Golding GB. 2006. Selection and slippage creating serine homopolymers. Mol Biol Evol 23: 2017-2025.
24. Karlin S, Brocchieri L, Bergman A, Mrazek J, Gentles AJ. 2002. Amino acid runs in eukaryotic proteomes and disease associations. Proc Natl Acad Sci 99: 333-338. (Pubitemid 34060363)
25. Kashi Y, King DG. 2006. Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22: 253-259.
26. Kim E, Magen A, Ast G. 2007. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 35: 125-131. (Pubitemid 46189837)
27. Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. 2003. Increase of functional diversity by alternative splicing. Trends Genet 19: 124-128. (Pubitemid 36279176)
28. Kruglyak S, Durrett RT, Schug MD, Aquadro CF. 1998. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci 95: 10774-10778. (Pubitemid 28413144)
29. Lev-Maor G, Goren A, Sela N, Kim E, Keren H, Doron-Faigenboim A, Leibman-Barak S, Pupko T, Ast G. 2007. The "alternative" choice of constitutive exons throughout evolution. PLoS Genet 3: e203. doi: 10.1371/journal.pgen.0030203.
30. Levinson G, Gutman GA. 1987. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221. (Pubitemid 17116759)
31. Lovell SC. 2003. Are non-functional, unfolded proteins ('junk proteins') common in the genome? FEBS Lett 554: 237-239.
32. Malko DB, Makeev VJ, Mironov AA, Gelfand MS. 2006. Evolution of exonintron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res 16: 505-509.
33. 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. (Pubitemid 36666928)
34. Mularoni L, Veitia RA, Alba MM. 2007. Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics 89: 316-325. (Pubitemid 46205127)
35. Ramensky VE, Nurtdinov RN, Neverov AD, Mironov AA, Gelfand MS. 2008. Positive selection in alternatively spliced exons of human genes. Am J Hum Genet 83: 94-98.
36. Rolfsmeier ML, Lahue RS. 2000. Stabilizing effects of interruptions on trinucleotide repeat expansions in Saccharomyces cerevisiae. Mol Cell Biol 20: 173-180.
37. Romero PR, Zaidi S, Fang YY, Uversky VN, Radivojac P, Oldfield CJ, Cortese MS, Sickmeier M, LeGall T, Obradovic Z, et al. 2006. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc Natl Acad Sci 103: 8390-8395. (Pubitemid 43838465)
38. Simon M, Hancock JM. 2009. Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins. Genome Biol 10: R59. doi: 10.1186/gb-2009-10-6-r59.
39. Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R. 2004. A non-EST-based method for exon-skipping prediction. Genome Res 14: 1617-1623.
40. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232. (Pubitemid 350100553)
41. Usdin K. 2008. The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases. Genome Res 18: 1011-1019. (Pubitemid 351931152)
42. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. (Pubitemid 352759009)
43. Wootton JC, Federhen S. 1993. Statistics of local complexity in amino acid sequences and sequence databases. Comput Chem 17: 149-163.
44. Xing Y, Lee C. 2005. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci 102: 13526-13531. (Pubitemid 41420882)
45. Xing Y, Lee C. 2006. Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7: 499-509. (Pubitemid 43943568)
46. Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, Hayashizaki Y, Gaasterland T. 2003. Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 13: 1290-1300. (Pubitemid 36827224)
47. Zhang XH, Chasin LA. 2006. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci 103: 13427-13432.
48. 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.