A Brief Review of Short Tandem Repeat Mutation

Genomics, Proteomics and Bioinformatics

Volumn 5, Issue 1, 2007, Pages 7-14

  Fan, Hao ^a,b   Chu, Jia You ^a  

^a INSTITUTE OF MEDICAL BIOLOGY   (China)

^b KUNMING MEDICAL UNIVERSITY   (China)

Author keywords

mutation; short tandem repeats

Indexed keywords

AGE; ARTICLE; DEGENERATIVE DISEASE; DNA POLYMORPHISM; DNA SEQUENCE; EUKARYOTE; MEIOSIS; MUTATION RATE; POPULATION GENETICS; SEX DIFFERENCE; SHORT TANDEM REPEAT; TRINUCLEOTIDE REPEAT;

EID: 34250211432     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(07)60009-6     Document Type: Review

References (59)

1. Tautz D. Notes on the defunction and nomenclature of tandemly repetitive DNA sequences. In: Pena S.D.J., et al. (Ed). DNA Fingerprinting: State of the Science (1993), Birkhauser Verlag, Basel, Switzerland 21-28
2. Koreth J., et al. Microsatellites and PCR ge-nomic analysis. J. Pathol. 178 (1996) 239-248
3. Ellegren H. Heterogeneous mutation processes in human microsatellite DNA sequences. Nat. Genet. 24 (2000) 400-402
4. Subramanian S., et al. Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 4 (2003) R13
5. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
6. Nadir E., et al. Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications. Proc. Natl. Acad. Sci. USA 93 (1996) 6470-6475
7. Urquhart A., et al. Variation in short tandem repeat sequences: a survey of twelve microsatellite loci for use as forensic identification markers. Int. J. Legal Med. 107 (1994) 13-20
8. Escher D., et al. Conservation of glutamine-rich transactivation function between yeast and humans. Mol. Cell. Biol. 20 (2000) 2774-2782
9. Gebhardt P., et al. Modulation of epidermal growth factor receptor gene transcription by a polymorphic dinucleotide repeat in intron 1. J. Biol. Chem. 274 (1999) 13176-13180
10. Meloni R., et al. A tetranucleotide polymorphic microsatellite, located in the first intron of the tyrosine hydroxylase gene, acts as a transcription regulatory element in vitro. Hum. Mol. Genet. 3 (1998) 423-428
11. Contente A., et al. A polymorphic microsatellite that mediates induction of PIGS by p53. Nat. Genet. 30 (2002) 315-320
12. Hamada H., et al. Enhanced gene expression by the poly(dT-dG).poly(dC-dA) sequence. Mol. Cell. Biol. 12 (1984) 2622-2630
13. Naylor L.H., and Clark E.M. d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. Nucleic Acids Res. 18 (1990) 1595-1601
14. Wahls W.P., et al. The Z-DNA motif d(TG)3o promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture. Mol. Cell. Biol. 10 (1990) 785-793
15. Wang Y.H., and Griffin J. Expanded CTG triplet blocks from myotonic dystrophy gene create the strongest known natural nucleosome positioning elements. Genomics 25 (1995) 570-573
16. Heale S.M., and Petes T.D. The stabilization of repetitive tracts of DNA by variant repeats requires a functional DNA mismatch repair system. Cell 83 (1995) 539-545
17. Huang Q.Y., et al. Mutation patterns at din-ucleotide microsatellite loci in humans. Am. J. Hum. Genet. 70 (2002) 625-634
18. Kayser M., et al. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am. J. Hum. Genet. 66 (2000) 1580-1588
19. Chakraborty R., et al. Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc. Natl. Acad. Sci. USA 94 (1997) 1041-1046
20. Di Rienzo A., et al. Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics 148 (1998) 1269-1284
21. Hastbacka J., et al. Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat. Genet. 2 (1992) 204-211
22. Holtkemper U., et al. Mutation rates at two human Y-chromosomal microsatellite loci using small pool PCR, techniques. Hum. Mol. Genet. 10 (2001) 629-633
23. Kornberg A., et al. Enzymatic synthesis of deoxyribonucleic acid. XVI. Oligonucleotides as templates and the mechanisms of their replication. Proc. Natl. Acad. Sci. USA 51 (1964) 315-323
24. Jobling M.A. 2004. The diversity of the human genome. In: Jobling M.A., et al. (Ed). Human Evolutionary Genetics: Origins. Peoples & Disease (2004), Garland Science, New York, USA 67
25. Schlotterer C., and Tautz D. Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 20 (1992) 211-215
26. Strand M., et al. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature 365 (1993) 274-276
27. Kruglyak S., et al. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc. Natl. Acad. Sci. USA 95 (1998) 10774-10778
28. Schlotterer C. Genome evolution: are mi-crosatellites really simple sequences?. Curr. Biol. 8 (1998) 132-134
29. Lai Y., and Sun F. The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol. Biol. Evol. 20 (2003) 2123-2131
30. Rose O., and Falush D. A threshold size for microsatellite expansion. Mol. Biol. Evol. 15 (1998) 613-615
31. Messier W., et al. The birth of microsatellites. Nature 381 (1996) 483
32. Kimura M., and Crow J.F. The number of al-leles that can be maintained in a finite population. Genetics 49 (1964) 725-738
33. Ota T., and Kimura M. A model of mutation appropriate to estimate the number of electrophoreti-cally detectable alleles in a finite population. Genet. Res. 22 (1973) 201-204
34. Shriver M.D., et al. VNTR, allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134 (1993) 983-993
35. Di Rienzo A., et al. Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res. 6 (1996) 211-217
36. Sajantila A., et al. Experimentally observed germline mutations at human micro-and minisatellite loci. Eur. J. Hum. Genet. 7 (1999) 263-266
37. Brinkmann B., et al. Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am. J. Hum. Genet. 62 (1998) 1408-1415
38. Goldstein D.B., and Clark A.G. Microsatellite variation in North American populations of Drosophila melanogaster. Nucleic Acids Res. 23 (1995) 3882-3886
39. Neef B.D., and Gross M.R. Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution 55 (2001) 1717-1733
40. Lee J.S., et al. Relative stabilities of dinucleotide and tetranucleotide repeats in cultured mammalian cells. Hum. Mol. Genet. 8 (1999) 2567-2572
41. Zhivotovsky L.A., et al. Biased mutations and microsatellite variation. Mol. Biol. Evol. 14 (1997) 926-933
42. Amos W., et al. Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR, ampliflability. Mol. Biol. Evol. 13 (1996) 1151-1154
43. Balloux F., et al. Microsatellite conservation, polymorphism, and GC content in shrews of the genus Sorex (Insectivora, Mammalia). Mol. Biol. Evol. 15 (1998) 473-475
44. Payseur B.A., and Nachman M.W. Microsatel-lite variation and recombination rate in the human genome. Genetics 156 (2000) 1285-1298
45. Shimmin L.C., et al. Male-driven evolution of DNA sequences. Nature 362 (1993) 745-747
46. Liu Q.Z. Chromosomal diseases. In: Li P. (Ed). Medical Genetics. second edition (2004), Peking Union Medical College Press, Beijing, China 153-155
47. Dib C., et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380 (1996) 152-154
48. Bowcock A., et al. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368 (1994) 455-457
49. Hammond H.A., et al. Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am. J. Hum. Genet. 55 (1994) 175-189
50. Edwards A., et al. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12 (1992) 241-253
51. Romualdi C., et al. Patterns of human diversity, within and among continents, inferred from bial-lelic DNA polymorphisms. Genome Res. 12 (2002) 602-612
52. Hardy O.J., et al. Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics 163 (2002) 1467-1482
53. Goldstein D.B., et al. An evaluation of genetic distances for use with microsatellite loci. Genetics 139 (1995) 463-471
54. Goldstein D.B., et al. Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA 92 (1995) 6723-6727
55. Nei M., and Takezaki N. The root of the phy-logenetic tree of human populations. Mol. Biol. Evol. 13 (1996) 170-177
56. Calafell P., et al. Short tandem repeat polymorphism evolution in humans. Eur. J. Hum. Genet. 6 (1998) 38-40
57. Jorde L.B., et al. The distribution of human genetic diversity: a comparison of mitochondrial, auto-somal, and Y-chromosome data. Am. J. Hum. Genet. 66 (2000) 979-988
58. Rosenberg N.A., et al. Genetic structure of human populations. Science 298 (2002) 2381-2385
59. Mountain J.L., et al. SNPSTR.s: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Res. 12 (2002) 1766-1772