Plant simple sequence repeats: Distribution, variation, and effects on gene expression

Genome

Volumn 51, Issue 2, 2008, Pages 79-90

  Sharopova, Natalya ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Gene expression; Gene function; mRNA transcript turnover; Regulation of transcription; Simple sequence repeats; SSR variation

Indexed keywords

TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BIOLOGY; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; PLANT; RICE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ARABIDOPSIS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PLANTS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; VARIATION (GENETICS);

ARABIDOPSIS; ZEA MAYS;

EID: 40749096523     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G07-110     Document Type: Article

References (42)

1. Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., et al. 2003. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science (Washington, D.C.), 301: 653-657. doi:10.1126/science.1086391.
2. Areshchenkova, T., and Ganal, M.W. 1999. Long tomato microsatellites are predominantly associated with centromeric regions. Genome, 42: 536-544. doi:10.1139/gen-42-3-536.
3. Armstrong, J.I., Yuan, S., Dale, J.M., Tanner, V.N., and Theologis, A. 2004. Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 101: 14978-14983. doi:10.1073/pnas.0404312101.
4. Berardini, T.Z., Mundodi, S., Reiser, L., Huala, E., Garcia-Hernandez, M., Zhang, P., et al. 2004. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 135: 745-755. doi:10.1104/pp.104.040071.
5. Bergmann, D.C., Lukowitz, W., and Somerville, C.R. 2004. Stomatal development and pattern controlled by a MAPKK kinase. Science (Washington, D.C.), 304: 1494-1497. doi:10.1126/science.1096014.
6. Chang, S., and Pikaard, C.S. 2005. Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J. Biol. Chem. 280: 796-804.
7. Cummings, C.J., and Zoghbi, H.Y. 2000. Trinucleotide repeats: mechanisms and pathophysiology. Annu. Rev. Genomics Hum. Genet. 1: 281-328. doi:10.1146/annurev.genom.1.1.281.
8. Dib, C., Faure, S., Fizames, C., Samson, D., Drouot, N., Vignal, A., et al. 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature (London), 380: 152-154. doi:10.1038/380152a0.
9. Doniger, S.W., Salomonis, N., Dahlquist, K.D., Vranizan, K., Lawlor, S.C., and Conklin, B.R. 2003. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4: R7. doi:10.1186/gb-2003-4-1-r7.
10. Ellegren, H. 2004. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5: 435-445. doi:10.1038/nrg1348.
11. Estoup, A., Jarne, P., and Cornuet, J.M. 2002. Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol. Ecol. 11: 1591-1604. doi:10.1046/j.1365-294X.2002.01576.x.
12. Fujimori, S., Washio, T., Higo, K., Ohtomo, Y., Murakami, K., Matsubara, K., et al. 2003. A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett. 554: 17-22. doi:10.1016/S0014-5793(03)01041-X.
13. Groenen, M.A., Crooijmans, R.P., Veenendaal, A., Cheng, H.H., Siwek, M., and van der Poel, J.J. 1998. A comprehensive microsatellite linkage map of the chicken genome. Genomics, 49: 265-274. doi:10.1006/geno.1998.5225.
14. Gutierrez, R.A., Ewing, R.M., Cherry, J.M., and Green, P.J. 2002. Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc. Natl. Acad. Sci. U.S.A. 99: 11513-11518. doi:10.1073/pnas.152204099.
15. Gyapay, G., Morissette, J., Vignal, A., Dib, C., Fizames, C., Millasseau, P., et al. 1994. The 1993-94 Généthon human genetic linkage map. Nat. Genet. 7: 246-339. doi:10.1038/ng0694supp-246.
16. Hirose, N., Makita, N., Kojima, M., Kamada-Nobusada, T., and Sakakibara, H. 2007. Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism. Plant Cell Physiol. 48: 523-539. doi:doi:10.1093/pcp/pcm022.
17. Ihara, N., Takasuga, A., Mizoshita, K., Takeda, H., Sugimoto, M., Mizoguchi, Y., et al. 2004. A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res. 14: 1987-1998. doi:10.1101/gr.2741704.
18. Kerr, M.K., Martin, M., and Churchill, G.A. 2000. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7: 819-837. doi:10.1089/10665270050514954.
19. Lasanthi-Kudahettige, R., Magneschi, L., Loreti, E., Gonzali, S., Licausi, F., Novi, G., et al. 2007. Transcript profiling of the anoxic rice coleoptile. Plant Physiol. 144: 218-231. doi:10.1104/pp.106.093997.
20. Lawson, M.J., and Zhang, L. 2006. Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol. 7: R14. doi:10.1186/gb-2006-7-2-r14.
21. Lee, B.H., Kapoor, A., Zhu, J., and Zhu, J.K. 2006. STABILIZED1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis. Plant Cell, 18: 1736-1749. doi:10.1105/tpc.106.042184.
22. Li, Y.C., Korol, A.B., Fahima, T., and Nevo, E. 2004. Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 21: 991-1007. doi:10.1093/molbev/msh073.
23. Lin, X., and Ashizawa, T. 2003. SCA10 and ATTCT repeat expansion: clinical features and molecular aspects. Cytogenet. Genome Res. 100: 184-188. doi:10.1159/000072853.
24. Morgante, M., Hanafey, M., and Powell, W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194-200. doi:10.1038/ng822.
25. Nemhauser, J.L., Mockler, T.C., and Chory, J. 2004. Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol 2: E258. doi:10.1371/journal.pbio.0020258.
26. Nishimura, M.T., Stein, M., Hou, B.-H., Vogel, J.P., Edwards, H., and Somerville, S.C. 2003. Loss of a callose synthase results in salicylic acid-dependent disease resistance. Science (Washington, D.C.), 301: 969-972. doi:10.1126/science.1086716.
27. Redman, J.C., Haas, B.J., Tanimoto, G., and Town, C.D. 2004. Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J. 38: 545-561. doi:10.1111/j.1365-313X.2004.02061.x.
28. Rocha, E.P., Matic, I., and Taddei, F. 2002. Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions? Nucleic Acids Res. 30: 1886-1894. doi:10.1093/nar/30.9.1886.
29. Saveliev, A., Everett, C., Sharpe, T., Webster, Z., and Festenstein, R. 2003. DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing. Nature (London), 422: 909-913. doi:10.1038/nature01596.
30. Sharopova, N., McMullen, M.D., Schultz, L., Schroeder, S., Sanchez-Villeda, H., Gardiner, J., et al. 2002. Development and mapping of SSR markers for maize. Plant Mol. Biol. 48: 463-481. doi:10.1023/A: 1014868625533.
31. Sharopova, N., Wen, T.-J., Lee, M., and Schnable, P. 1999. Abundance and variation of imperfect simple sequence repeats in maize ESTs. In Proceedings of the 41st Annual Maize Genetics Conference, 11-14 March 1999, Lake Geneva, Wis. Edited by R. Brown, B. Boston, K. Dawe, A. Kriz, J. Langdale, M. McMullen, et al.
32. Somers, D.J., Isaac, P., and Edwards, K. 2004. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 109: 1105-1114. doi:10.1007/s00122-004-1740-7.
33. Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., and McCouch, S. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452. doi:10.1101/gr.184001.
34. Toth, G., Gaspari, Z., and Jurka, J. 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 10: 967-981. doi:10.1101/gr.10.7.967.
35. Verstrepen, K.J., Jansen, A., Lewitter, F., and Fink, G.R. 2005. Intragenic tandem repeats generate functional variability. Nat. Genet. 37: 986-990. doi:10.1038/ng1618.
36. Vigouroux, Y., McMullen, M., Hittinger, C.T., Houchins, K., Schulz, L., Kresovich, S., et al. 2002. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc. Natl. Acad. Sci. U.S.A. 99: 9650-9655. doi:10.1073/pnas.112324299.
37. Walia, H., Wilson, C., Condamine, P., Liu, X., Ismail, A.M., Zeng, L., et al. 2005. Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol. 139: 822-835. doi:10.1104/pp.105.065961.
38. Wang, H.-J., Wan, A.-R., Hsu, C.-M., Lee, K.-W., Yu, S.-M., and Jauh, G.-Y. 2007. Transcriptomic adaptations in rice suspension cells under sucrose starvation. Plant Mol. Biol. 63: 441-463. doi:10.1007/s11103-006-9100-4.
39. Watanabe, T.K., Bihoreau, M.T., McCarthy, L.C., Kiguwa, S.L., Hishigaki, H., Tsuji, A., et al. 1999. A radiation hybrid map of the rat genome containing 5,255 markers. Nat. Genet. 22: 27-36.
40. Yamada, N.A., Smith, G.A., Castro, A., Roques, C.N., Boyer, J.C., and Farber, R.A. 2002. Relative rates of insertion and deletion mutations in dinucleotide repeats of various lengths in mismatch repair proficient mouse and mismatch repair deficient human cells. Mutat. Res. 499: 213-225.
41. Yang, Y., Buckley, M., Dudoit, S., and Speed, T. 2000. Comparison of methods for image analysis on cDNA microarray data. In Technical Report 2000. Statistics Department, University of California, Berkley.
42. Zeevi, M., Nevins, J.R., and Darnell, J.E., Jr. 1982. Newly formed mRNA lacking polyadenylic acid enters the cytoplasm and the polyribosomes but has a shorter half-life in the absence of polyadenylic acid. Mol. Cell. Biol. 2: 517-525.