Bioinformatic Analysis of Evolutional Conservatism and Functional Significance of Microsatellite Alleles of Human 14Q13.2 Region Associated with Type 2 Diabetes Mellitus

Proceedings of the Latvian Academy of Sciences, Section B: Natural, Exact, and Applied Sciences

Volumn 62, Issue 3, 2008, Pages 91-102

  Sjakste, Tatjana ^a   Pîrâgs, Valdis ^a   Sjakste, Nikolajs ^a   Poud, Ilvapiunas ^a   Lazdiòð, Mâris ^a  

^a UNIVERSITY OF LATVIA   (Latvia)

Author keywords

bioinformatics; Chromosome 14; evolution; microsatellites; polymorphism; proteasomes; PSMA6; type 2 diabetes mellitus

Indexed keywords

EID: 85007093728     PISSN: 1407009X     EISSN: None     Source Type: Journal    
DOI: 10.2478/v10046-008-0001-6     Document Type: Article

References (31)

1. Coux, O., Nothwang, H.G., Silva Pereira, I., Recillas Targa, F., Bey, F., Scherrer, K. (1994). Phylogenic relationships of the amino acid sequences of prosome (proteasome, MCP) subunits. Mol. Gen. Genet., 245, 769-780.
2. Epplen, C., Santos, E.J., Maueler, W., van Helden, P., Epplen, J.T. (1997). On simple repetitive DNA sequences and complex diseases. Electrophoresis, 18, 1577-1585.
3. Excoffier, L., Laval, G., Schneider, S. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
4. Gabellini, N. (2001). A polymorphic GT repeat from the human cardiac Na+Ca2+ exchanger intron 2 activates splicing. Eur. J. Biochem., 268, 1076-1083.
5. Galande, S. (2002) Chromatic (dis)organization and cancer: BUR-binding proteins as biomarkers for cancer. Curr.Cancer Drug Targets, 2, 157-190.
6. Gebhard, F., Zänker, K.S., Brandt, B. (1999). Modulation of epidermal growth factor receptor gene transcription by a polymorphic dinucleotide repeat in intron 1. J. Biol. Chem., 274, 13176-13180.
7. Grant, S.F., Thorleifsson, G., Reynisdottir, I., Benediktsson, R., Manolescu, A., Sainz, J., Helgason, A., Stefansson, H., Emilsson, V., Helgadottir, A., Styrkarsdottir, U., Magnusson, K.P., Walters, G.B., Palsdottir, E., Jonsdottir, T., Gudmundsdottir, T., Gylfason, A., Saemundsdottir, J., Wilensky, R.L., Reilly, M.P., Rader, D.J., Bagger, Y., Christiansen, C., Gudnason, V., Sigurdsson, G., Thorsteinsdottir, U., Gulcher, J.R., Kong, A., Stefansson, K. (2006). Variant of transcription factor 7 - like 2 (TCF7L2) gene confers risk of type 2 diabetes. Nat. Genet., 38, 320-323.
8. Grossi de Sa, M.-F., Martins de Sa, C., Harper, F., Olink-Coux, M., Huesca, M., Scherrer K. (1988). The association of prosomes with some of the intermediate filament networks of the animal cell. J. Cell Biol., 107, 1517-1530.
9. Horikawa, Y., Oda, N., Cox, N.J. (2000). Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat. Genet., 26, 135-137.
10. Hui. J., Hung, L.H., Heiner, M., Schreiner, S., Neumuller, N., Reither, G., Haas S.A., Bindereif, A. (2005). Intronic CA-repeat and CA-rich elements: Anew class of regulators of mammalian alternative splicing. EMBO (European Molecular Biology Organisation) J., 24, 1988-1998.
11. Hui, J., Reither, G., Bindereif, A. (2003). Novel functional role of CA repeats and hnRNP L in RNA stability. RNA, 9, 931-936.
12. Kashi, Y., King, D.G. (2006). Simple sequence repeats as advantageous mutators in evolution. Trends Genet., 22, 253-259.
13. Larsen, A., Weintraub, H. (1982). An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell, 29, 609-622.
14. Majewski, J., Ott, J. (2000). GT repeats are associated with recombination on human chromosome 22. Gen. Res., 10, 1108-1114.
15. Ozaki, K., Sato, H., Iida, A., Mizuno, H., Nakamura, T., Miyamoto, Y., Takahashi, A., Tsunoda, T., Ikegawa, S., Kamatani, N., Hori, M., Nakamura, Y., Tanaka, T. (2006). A functional SNP in PSMA6 confers risk of myocardial infarction in the Japanese population. Nat. Genet., 38, 921-925.
16. Rana, N.A., Ebenezer, N.D., Webster A.R., Linares A.R., Whitehouse D.B., Povey S., Hardcastle A.J. (2004). Recombination hotspots and block structure of linkage disequilibrium in the human genome exemplified by detailed analysis of PGM1 on 1p31. Hum. Mol. Genet., 13, 3089-3102.
17. Recillas-Targa, F., Razin, S. V., de Moura Gallo, C. V., Scherrer, K. (1994). Excision close to matrix attachment regions of the whole domain of the chicken alpha-globin gene domain by nuclease S1 and characterisation of the framing structures. Proc. Natl. Acad. Sci. USA, 91, 4422-4426.
18. Rome, S., Meugnier, E., Vidal, H., (2004). The ubiquitin-proteasome pathway is a new partner for the control of insulin signaling. Curr. Opin. Clin. Nutr. Metab. Care, 7, 249-254.
19. Sharma, V.K., B-Rao, C., Sharma, A., Brahmachari, S.K., Ramachandran, S. (2003). (TG:CA)(n) repeats in human housekeeping genes. J. Biomol. Struct. Dyn., 21, 303-310.
20. Sharma, V.K., Brahmachari, S.K., Ramachandar, S. (2005a) (TG/CA)n repeats in human gene families: Abundance and selective patters of distribution according to function and gene length. BMC Genomics, 6, 83.
21. Sharma, S., Rajan, U.M., Kumar, A., Soni, A., Ghosh, B. (2005b). A novel (TG)n(GA)m repeat polymorphism 254 bp downstream of the mast cell chymase (CMA1) gene is associated with atopic asthma and total serum IgE levels. J. Hum. Genet., 50, 276-282.
22. Sjakste, N.I., Sjakste, T.G. (2002). Structure of globin gene domains in mammals and birds. Russ. J. Genet., 38(12), 1342-1358.
23. Sjakste, N.I., Sjakste, T.G. (2007a). Possible involvement of DNA breaks in epigenetic regulationof cell differentiation. Russ. J. Genet., 43(5), 467-484.
24. Sjakste, N., Sjakste, T. (2007b). Possible involvement of DNA strand breaks in regulation of cell differentiation. Eur. J. Histochem, 51, 81-94.
25. Sjakste, T., Eglite, J., Sochnevs, A., Marga, M., Pirags, V., Collan, Y., Sjakste N. (2004). Microsatellite genotyping of chromosome 14q13.2-14q13 in the vicinity of proteasomal gene PSMA6 and association with Graves' disease in the Latvian population. Immunogenetics, 56, 238-243.
26. Sjakste, T., Kalis, M., Poudziuas, I., Pirags, V., Lazdins, M., Groop, L., Sjakste, N. (2007a). Association of microsatellite polymorphisms of the human 14q13.2 region with type 2 diabetes mellitus in Latvian and Finnish populations. Ann. Human Genet., 71, 772-776.
27. Sjakste, T., Poudziunas, I., Ninio, E., Perret, C., Pirags, V., Nicaud, V., Lazdins, M., Evans, A., Morrison, C., Cambien, F., Sjakste N. (2007b). SNPs of PSMA6 gene-investigation of possible association with myocardial infarction and type 2 diabetes mellitus. Russ. J. Genet., 43, 442-448.
28. Stallings, R.L., Ford, A.F., Nelson, D., Torney, D.C., Hildebrand, C.E., Moyzis, R.K. (1991). Evolution and distribution of (GT)n repetitive sequences in mammalian genomes. Genomics, 10, 807-815.
29. Tolstonog, G.V., Mothes, E., Shoeman, R.L., Traub, P. (2001). Isolation of SDS-stable complexes of the intermediate filament protein vimentin with repetitive, mobile, nuclear matrix attachment region, and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts. DNA Cell. Biol., 20, 531-554.
30. Tolstonog, G.V., Li, G., Shoeman, R.L., Traub, P. (2005). Interaction in vitro of type III intermediate filament proteins with higher order structures of single-stranded DNA, particularly with G-quadruplex DNA. DNA Cell Biol., 24, 85-110.
31. Tsunoda, T., Lathrop, G.M., Sekine, A., Yamada, R., Takahashi, A., Ohnishi, Y., Tanaka, T., Nakamura, Y. (2004). Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome. Hum. Mol. Genetics, 13, 1623-1632.