Loris Mularoni, Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain
Macarena Toll‐Riera, Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain
M Mar Albà, Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain
Published online: May 2008
DOI: 10.1002/9780470015902.a0020844
The genome of humans and other apes shows important differences in trinucleotide repeat sequences. This has implications for the evolution of protein function and susceptibility to repeat expansion disease.
Keywords: microsatellites; trinucleotide repeats; triplet expansion disease; homopeptides
|
Figure 1. Alignments of protein regions containing human disease-associated repeats. The sequence at the top corresponds to the human sequence and the one at the bottom to the orthologous chimpanzee sequence. See Table
|
| References | |
| Alba MM and Guigo R (2004) Comparative analysis of amino acid repeats in rodents and humans. Genome Research 14(4): 549–554. | |
| Alba MM, Santibanez-Koref MF and Hancock JM (1999) Conservation of polyglutamine tract size between mice and humans depends on codon interruption. Molecular Biology and Evolution 16(11): 1641–1644. | |
| book Alba MM, Tompa P and Veitia RA (2007) "Amino acid repeats and the structure and evolution of proteins". In: Volff J-N (ed.) Gene and Protein Evolution pp. 119–130. Basel: Karger. | |
| Amiel J, Trochet D, Clement-Ziza M, Munnich A and Lyonnet S (2004) Polyalanine expansions in human. Human Molecular Genetics 13(Spec. no. 2): R235–R243. | |
| Anan K, Yoshida N, Kataoka Y et al. (2007) Morphological change caused by loss of the taxon-specific polyalanine tract in Hoxd-13. Molecular Biology and Evolution 24(1): 281–287. | |
| Andres AM, Lao O, Soldevila M, Calafell F and Bertranpetit J (2003a) Dynamics of CAG repeat loci revealed by the analysis of their variability. Human Mutation 21(1): 61–70. | |
| Andres AM, Soldevila M, Lao O et al. (2004) Comparative genetics of functional trinucleotide tandem repeats in humans and apes. Journal of Molecular Evolution 59(3): 329–339. | |
| Andres AM, Soldevila M, Saitou N et al. (2003b) Understanding the dynamics of Spinocerebellar Ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes. Neuroscience Letters 336(3): 143–146. | |
| Borstnik B and Pumpernik D (2002) Tandem repeats in protein coding regions of primate genes. Genome Research 12(6): 909–915. | |
| Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proceedings of the National Academy of Sciences of the USA 99(21): 13633–13635. | |
| Brown LY and Brown SA (2004) Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends in Genetics 20(1): 51–58. | |
| Butland SL, Devon RS, Huang Y et al. (2007) CAG-encoded polyglutamine length polymorphism in the human genome. BMC Genomics 8: 126. | |
| Caburet S, Cocquet J, Vaiman D and Veitia RA (2005) Coding repeats and evolutionary “agility”. BioEssays 27(6): 581–587. | |
| Choong CS, Kemppainen JA and Wilson EM (1998) Evolution of the primate androgen receptor: a structural basis for disease. Journal of Molecualr Evolution 47(3): 334–342. | |
| Clark RM, Bhaskar SS, Miyahara M, Dalgliesh GL and Bidichandani SI (2006) Expansion of GAA trinucleotide repeats in mammals. Genomics 87(1): 57–67. | |
| Consortium TCSaA (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437(7055): 69–87. | |
| Cooper G, Rubinsztein DC and Amos W (1998) Ascertainment bias cannot entirely account for human microsatellites being longer than their chimpanzee homologues. Human Molecular Genetics 7(9): 1425–1429. | |
| Ellegren H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nature Genetics 24(4): 400–402. | |
| Ellegren H, Primmer CR and Sheldon BC (1995) Microsatellite ‘evolution’: directionality or bias? Nature Genetics 11(4): 360–362. | |
| Fondon JW 3rd and Garner HR (2004) Molecular origins of rapid and continuous morphological evolution. Proceedings of the National Academy of Sciences of the USA 101(52): 18058–18063. | |
| Forbes SH, Hogg JT, Buchanan FC, Crawford AM and Allendorf FW (1995) Microsatellite evolution in congeneric mammals: domestic and bighorn sheep. Molecular Biology and Evolution 12(6): 1106–1113. | |
| Galant R and Carroll SB (2002) Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415(6874): 910–913. | |
| Gatchel JR and Zoghbi HY (2005) Diseases of unstable repeat expansion: mechanisms and common principles. Nature Reviews. Genetics 6(10): 743–755. | |
| Gerber HP, Seipel K, Georgiev O et al. (1994) Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science 263(5148): 808–811. | |
| Glazko GV and Nei M (2003) Estimation of divergence times for major lineages of primate species. Molecular Biology and Evolution 20(3): 424–434. | |
| Green H and Wang N (1994) Codon reiteration and the evolution of proteins. Proceedings of the National Academy of Sciences of the USA 91(10): 4298–4302. | |
| Hancock JM and Simon M (2005) Simple sequence repeats in proteins and their significance for network evolution. Gene 345(1): 113–118. | |
| Hancock JM, Worthey EA and 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. Molecular Biology and Evolution 18(6): 1014–1023. | |
| Hong KW, Hibino E, Takenaka O et al. (2006) Comparison of androgen receptor CAG and GGN repeat length polymorphism in humans and apes. Primates 47(3): 248–254. | |
| Hsing AW, Gao YT, Wu G et al. (2000) Polymorphic CAG and GGN repeat lengths in the androgen receptor gene and prostate cancer risk: a population-based case-control study in China. Cancer Research 60(18): 5111–5116. | |
| Hubbard T, Andrews D, Caccamo M et al. (2005) Ensembl 2005. Nucleic Acids Research 33(Database issue): D447–D453. | |
| Huntley MA and Clark AG (2007) Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species. Molecular Biology and Evolution 24(12): 2598–2609. | |
| Jodice C, Giovannone B, Calabresi V et al. (1997) Population variation analysis at nine loci containing expressed trinucleotide repeats. Annals of Human Genetics 61(Pt 5): 425–438. | |
| Karlin S, Brocchieri L, Bergman A, Mrazek J and Gentles AJ (2002) Amino acid runs in eukaryotic proteomes and disease associations. Proceedings of the National Academy of Sciences of the USA 99(1): 333–338. | |
| Kashi Y and King DG (2006) Simple sequence repeats as advantageous mutators in evolution. Trends in Genetics 22(5): 253–259. | |
| Kehrer-Sawatzki H and Cooper DN (2007) Understanding the recent evolution of the human genome: insights from human–chimpanzee genome comparisons. Human Mutation 28(2): 99–130. | |
| Kumar S, Filipski A, Swarna V, Walker A and Hedges SB (2005) Placing confidence limits on the molecular age of the human–chimpanzee divergence. Proceedings of the National Academy of Sciences of the USA 102(52): 18842–18847. | |
| Lander ES, Linton LM, Birren B et al. (2001) Initial sequencing and analysis of the human genome. Nature 409(6822): 860–921. | |
| Lanz RB, Wieland S, Hug M and Rusconi S (1995) A transcriptional repressor obtained by alternative translation of a trinucleotide repeat. Nucleic Acids Research 23(1): 138–145. | |
| Leakey MG, Feibel CS, McDougall I, Ward C and Walker A (1998) New specimens and confirmation of an early age for Australopithecus anamensis. Nature 393(6680): 62–66. | |
| Levinson G and Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution 4(3): 203–221. | |
| Messer PW and Arndt PF (2007) The majority of recent short DNA insertions in the human genome are tandem duplications. Molecular Biology and Evolution 24(5): 1190–1197. | |
| Mularoni L, Guigo R and Alba MM (2006) Mutation patterns of amino acid tandem repeats in the human proteome. Genome Biology 7(4): R33. | |
| Mularoni L, Veitia RA and Alba MM (2007) Highly constrained proteins contain an unexpectedly large number of amino acid tandem repeats. Genomics 89(3): 316–325. | |
| O'Dushlaine CT, Edwards RJ, Park SD and Shields DC (2005) Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biology 6(8): R69. | |
| Primmer CR and Ellegren H (1998) Patterns of molecular evolution in avian microsatellites. Molecular Biology and Evolution 15(8): 997–1008. | |
| Puente XS, Velasco G, Gutierrez-Fernandez A et al. (2006) Comparative analysis of cancer genes in the human and chimpanzee genomes. BMC Genomics 7(1): 15. | |
| Rozanska M, Sobczak K, Jasinska A et al. (2007) CAG and CTG repeat polymorphism in exons of human genes shows distinct features at the expandable loci. Human Mutation 28(5): 451–458. | |
| Rubinsztein DC, Amos W, Leggo J et al. (1995a) Microsatellite evolution – evidence for directionality and variation in rate between species. Nature Genetics 10(3): 337–343. | |
| Rubinsztein DC, Leggo J and Amos W (1995b) Microsatellites evolve more rapidly in humans than in chimpanzees. Genomics 30(3): 610–612. | |
| Rubinsztein DC, Leggo J, Coetzee GA et al. (1995c) Sequence variation and size ranges of CAG repeats in the Machado–Joseph disease, spinocerebellar ataxia type 1 and androgen receptor genes. Human Molecular Genetics 4(9): 1585–1590. | |
| Shimohata M, Shimohata T, Igarashi S, Naruse S and Tsuji S (2005) Interference of CREB-dependent transcriptional activation by expanded polyglutamine stretches – augmentation of transcriptional activation as a potential therapeutic strategy for polyglutamine diseases. Journal of Neurochemistry 93(3): 654–663. | |
| Tautz D and Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research 12(10): 4127–4138. | |
| Toth G, Gaspari Z and Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research 10(7): 967–981. | |
| Vowles EJ and Amos W (2006) Quantifying ascertainment bias and species-specific length differences in human and chimpanzee microsatellites using genome sequences. Molecular Biology and Evolution 23(3): 598–607. | |
| Warren ST (1997) Polyalanine expansion in synpolydactyly might result from unequal crossing-over of HOXD13. Science 275(5298): 408–409. | |
| Webster MT, Smith NG and Ellegren H (2002) Microsatellite evolution inferred from human–chimpanzee genomic sequence alignments. Proceedings of the National Academy of Sciences of the USA 99(13): 8748–8753. | |
| Wren JD, Forgacs E, Fondon JW III et al. (2000) Repeat polymorphisms within gene regions: phenotypic and evolutionary implications. American Journal of Human Genetics 67(2): 345–356. | |
| Further Reading | |
| book Fry M and Usdin K (eds) (2006) Human Nucleotide Expansion Disorders (Nucleic Acids and Molecular Biology). Berlin: Springer. | |
| book Goldstein DB and Schlotterer C (eds) (1999) Microsatellites: Evolution and Applications. Oxford, UK: Oxford University Press. | |
| book Li W-H (2006) Molecular Evolution. Sunderland: Sinauer Associates Inc. | |
| book Rubinsztein D (1998) Analysis of Triplet Repeat Disorders (Human Molecular Genetics). London, UK: Garland Science. | |
| book Yang Z (2006) Computational Molecular Evolution. Oxford, UK: Oxford University Press. | |
Copyright © 2000-2013 by John Wiley & Sons, Inc., or related companies. All rights reserved.
