Tandemly repeated trinucleotides - comparative analysis
Languages of publication
Characteristics of 64 possible tandem trinucleotide repeats (TSSR) from Homo sapiens (hs), Mus musculus (mm) and Rattus norvegicus (rn) genomes are presented. Comparative analysis of TSSR frequency depending on their repetitiveness and similarity of the TSSR length distributions is shown. Comparative analysis of TSSR sequence motifs and association between type of motif and its length (n) using ρ-coefficient method (quantitatively measuring the association between variables in contingency tables) is presented. These analyses were carried out in the context of neurodegenerative diseases based on trinucleotide tandems. The length of these tandems and their relation to other TSSR is estimated. It was found that the higher repetitiveness (n) the lower frequency of trinucleotides tandems. Differences between genomes under consideration, especially in longer than n=9 TSSR were discussed. A significantly higher frequency off A- and T-rich tandems is observed in the human genome (as well as in human mRNA). This observation also applies to mm and rn, although lower abundant in proportion to human genomes was found. The origin of elongation (or shortening) of TSSR seems to be neither frequency nor length dependent. The results of TSSR analysis presented in this work suggest that neurodegenerative disease-related microsatellites do not differ versus the other except the lower frequency versus the other TSSR. CAG occurs with relatively high frequency in human mRNA, although there are other TSSR with higher frequency that do not cause comparable disease disorders. It suggests that the mechanism of TSSR instability is not the only origin of neurodegenerative diseases.
- Ashley CT, Warren ST (1995) Trinucleotide repeat expansion and human disease. Annu Rev Genet 29: 703-728.
- Beckman JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12: 627-631.
- Bickeboller H, Clerget-Drapoux F (1995) Statistical properties of the allelic and genotypic transmission/disequilibrium test for multiallelic markers. Genet Epidemiol 12: 865-870.
- Björnstad JF (1979) Inference theory in contingency tables. Statistical Research Report Oslo pp 1-26.
- Dowsing AT, Yong EL, Clark M, McLachlan RI, Kretser DM, Trounson OA (1999) Linkage between male infertility and trinucleotide repeat expansion in the androgen-receptor gene. Lancet 354: 640-643.
- Everett CM, Wood NW (2004) Trinucleotide repeats and neurodegenerative disease. Brain 127(Pt 11): 2385-2405.
- Goetz CG, Pappert EJ (1999) Textbook of Clinical Neurology. W.B. Sounders Company, Philadelphia, London, Toronto, Montreal, Sydney, Tokyo.
- Goodman LA, Kruskal WH (1954) Measures of association for cross classifications.J Am Stat Assoc 49: 732-764.
- Goodman LA, Kruskal WH (1959) Measures of association for cross classifications. II: Further discussion and references. J Am Stat Assoc 54: 123-163.
- Goodman LA, Kruskal WH (1963) Measures of association for cross classifications. III: Approximate sampling theory. J Am Stat Assoc 58: 310-364.
- Goodman LA, Kruskal WH (1972) Measures of association for cross classifications. IV. Simplification of asymptotic variances. J Am Stat Assoc 67: 415-421.
- Grewal RP (1999) Neurodegeneration in Xeroderma Pigmentosum: a trinucleotide repeat mutation analysis. J Neurol Sci 163: 183-186
- Gusella JF, MacDonald ME (1996) Trinucleotide instability: a repeating theme in human inherited disorders. Annu Rev Med 47: 201-9.
- Gsur A, Preyer M, Haidinger G, Zidek T, Madersbacher S, Schatzl G, Marberger M, Vutuc C, Micksche M (2002) Polymorphic CAG repeats in the androgen receptor gene, prostate-specific antigen polymorphism and prostate cancer risk. Carcinogenesis 23: 1647-1651.
- Hartenstine MJ, Goodman MF, Petruska J (2000) Base stacking and even/odd behaviour of harpin loops in DNA polymerase. J Biol Chem 275: 18382-18390.
- Jurka J, Pethiyagoda C (1995) Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol 40: 120-126.
- Kovtun IV, McMurray CT (2001) Trinucleotide expansion in haploid germ cells by gap repair. Nat Genet 27: 407-411.
- Kruglyak S, Durret RT, Schug MD, Aquadro CF (1998) Equilibrium distribution of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci USA 95: 10774-10778.
- Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4: 203-221.
- Margolis RL, Abraham MR, Gatchell S, Li SH, Kidwai AS, Breschel TS, Stine OC, Callahan C, McInnis MG, Ross CA (1997) cDNAs with long CAG trinucleotide repeats from human brain. Hum Genet 100: 114-122.
- Pearson CE, Ewel A, Acharya S, Fishel RA, Sinden RR (1997) Human MSH2 binds to trinucleotide repeat DNA structures associated with neurodegenerative diseases. Hum Mol Genet 6: 1117-1123.
- Schlotterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20: 211-215.
- Sinden RR, Potaman VN, Oussatcheva EA, Pearson CE, Lyubchenko YL, Shlyakhtenko LS (2002) Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. J Biosci 27: 53-65.
- Strom SS, Gu Y, Zhang H, Troncoso P, Babaian RJ, Pettaway CA, Shete S, Spitz MR, Logothetis CJ (2004) Androgen receptor polymorphisms and risk of biochemical failure among prostatectomy patients. Prostate 60: 343-351.
- Strachan T, Read AP (1999) Human Molecular Genetics 2 2nd edn. BIOS Scientific Publishers Ltd, Oxford, UK.
- Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10: 967-981.
- Waterston RH, Lindblad-Toh K, Birney E, Rogers J, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
- Yandava CN, Gastier JM, Pulido JC, Brody T, Sheffield V, Murray J, Buetow K, Duyk GM (1997) Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites. Genome Res 7: 716-724.
Publication order reference