Homolog-specific PCR primer design for profiling splice variants

Nucleic Acids Research

Volumn 39, Issue 10, 2011, Pages

  Srivastava, Gyan Prakash ^a,b   Hanumappa, Mamatha ^a,c   Kushwaha, Garima ^a   Nguyen, Henry T ^a   Xu, Dong ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABIOTIC STRESS; ARTICLE; COMPUTER PROGRAM; GENE AMPLIFICATION; GENE DUPLICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC VARIABILITY; INFORMATION RETRIEVAL; MULTIGENE FAMILY; NONHUMAN; PLANT GENE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA SPLICING; SEQUENCE HOMOLOGY; SOYBEAN; ALGORITHM; ALTERNATIVE RNA SPLICING; CHEMISTRY; GENETICS; VALIDATION STUDY;

GLYCINE MAX;

ISOPROTEIN; PRIMER DNA;

ALGORITHMS; ALTERNATIVE SPLICING; DNA PRIMERS; POLYMERASE CHAIN REACTION; PROTEIN ISOFORMS; SOFTWARE; SOYBEANS;

EID: 79961178914     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr127     Document Type: Article

References (42)

1. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921. (Pubitemid 32165345)
2. Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R. and Shoemaker, D.D. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141-2144. (Pubitemid 38017950)
3. Strehler, E.E. and Zacharias, D.A. (2001) Role of alternative splicing in generating isoform diversity among plasma membrane calcium pumps. Phys. Rev., 81, 21-50. (Pubitemid 32096172)
4. Muro, A.F., Iaconcig, A. and Baralle, F.E. (1998) Regulation of the fibronectin EDA exon alternative splicing. Cooperative role of the exonic enhancer element and the 50 splicing site. FEBS Lett., 437, 137-141. (Pubitemid 28498256)
5. Lou, H. and Gagel, R.F. (1998) Alternative RNA processing-its role in regulating expression of calcitonin/calcitonin gene-related peptide. J. Endocrinol., 156, 401-405. (Pubitemid 28131456)
6. Hwu, W.L., Yeh, H.Y., Fang, S.W., Chiang, H.S., Chiou, Y.W. and Lee, Y.M. (2003) Regulation of GTP cyclohydrolase I by alternative splicing in mononuclear cells. Biochem. Biophys. Res. Commun., 306, 937-942.
7. Garcia-Blanco, M.A., Baraniak, A.P. and Lasda, E.L. (2004) Alternative splicing in disease and therapy. Nature Biotechnol., 22, 535-546. (Pubitemid 38585905)
8. Faustino, N.A. and Cooper, T.A. (2003) Pre-mRNA splicing and human disease. Genes Develop., 17, 419-437. (Pubitemid 36258756)
9. Xu, Q. and Lee, C. (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res., 31, 5635-5643. (Pubitemid 37441935)
10. Mano, S., Hayashi, M. and Nishimura, M. (2000) A leaf-peroxisomal protein, hydroxypyruvate reductase, is produced by light-regulated alternative splicing. Cell Biochem. Biophys., 32, 147-154.
11. Zhang, X.N. and Mount, S.M. (2009) Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol., 150, 1450-1458.
12. Dinesh-Kumar, S.P. and Baker, B.J. (2000) Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance. Proc. Natl Acad. Sci. USA, 97, 1908-1913. (Pubitemid 30118542)
13. Filichkin, S.A., Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E., Wong, W.K. and Mockler, T.C. (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res., 20, 45-58.
14. Campbell, M.A., Haas, B.J., Hamilton, J.P., Mount, S.M. and Buell, C.R. (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics, 7, 327.
15. Wang, B.B. and Brendel, V. (2006) Genomewide comparative analysis of alternative splicing in plants. Proc. Natl Acad. Sci. USA, 103, 7175-7180.
16. Veistinen, E., Liippo, J. and Lassila, O. (2002) Quantification of human Aiolos splice variants by real-time PCR. J. Immunol. Methods, 271, 113-123. (Pubitemid 35346372)
17. Sun, L. and Irudayaraj, J. (2009) PCR-free quantification of multiple splice variants in a cancer gene by surface-enhanced Raman spectroscopy. J. Phys. Chem. B, 113, 14021-14025.
18. Taveau, M., Stockholm, D., Spencer, M. and Richard, I. (2002) Quantification of splice variants using molecular beacon or scorpion primers. Anal. Biochem., 305, 227-235. (Pubitemid 34666795)
19. Mavrogiannou, E., Strati, A., Stathopoulou, A., Tsaroucha, E.G., Kaklamanis, L. and Lianidou, E.S. (2007) Real-time RT-PCR quantification of human telomerase reverse transcriptase splice variants in tumor cell lines and non-small cell lung cancer. Clin. Chem., 53, 53-61. (Pubitemid 46047763)
20. Vandenbroucke, I.I, Vandesompele, J., Paepe, A.D. and Messiaen, L. (2001) Quantification of splice variants using real-time PCR. Nucleic Acids Res., 29, E68.
21. Srivastava, G.P., Guo, J., Shi, H. and Xu, D. (2008) PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics, 24, 1837-1842.
22. Xu, D., Li, G., Wu, L., Zhou, J. and Xu, Y. (2002) PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics, 18, 1432-1437. (Pubitemid 35414533)
23. Srivastava, G.P. and Xu, D. (2007) Genome-scale probe and primer design with PRIMEGENS. Methods Mol. Biol., 402, 159-176.
24. Arvidsson, S., Kwasniewski, M., Riano-Pachon, D.M. and Mueller-Roeber, B. (2008) QuantPrime-a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics, 9, 465.
25. Lalitha, S. (2000) Primer Premier 5. Biotech. Software & Internet Rep., 1, 270-272.
26. Apte, A. and Singh, S. (2007) AlleleID: a pathogen detection and identification system. Methods Mol. Biol., 402, 329-346.
27. Sandhu, K.S. and Acharya, K.K. (2005) ExPrimer: to design primers from exon-exon junctions. Bioinformatics, 21, 2091-2092. (Pubitemid 40668051)
28. Ryan, M.C., Zeeberg, B.R., Caplen, N.J., Cleland, J.A., Kahn, A.B., Liu, H. and Weinstein, J.N. (2008) SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics, 9, 313.
29. Huang, X.Q. and Brule-Babel, A. (2010) Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples. BMC Res. Notes, 3, 140.
30. Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
31. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
32. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol.: J. Comput. Mol. Cell Biol., 7, 203-214. (Pubitemid 30412170)
33. Schuler, G.D. (1997) Sequence mapping by electronic PCR. Genome Res., 7, 541-550. (Pubitemid 27232016)
34. Shoemaker, R.C., Polzin, K., Labate, J., Specht, J., Brummer, E.C., Olson, T., Young, N., Concibido, V., Wilcox, J., Tamulonis, J.P. et al. (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics, 144, 329-338. (Pubitemid 26291940)
35. Goldblatt, P. (1981) Cytology and phylogeny of leguminosae. In Polhill, R.M. and Raven, P.H. (eds), Advances in Legume Systematics, Part 2. Royal Botanic Gardens, Kew, pp. 427-463.
36. Schlueter, J.A., Dixon, P., Granger, C., Grant, D., Clark, L., Doyle, J.J. and Shoemaker, R.C. (2004) Mining EST databases to resolve evolutionary events in major crop species. Genome/Natl Res. Council Canada, 47, 868-876. (Pubitemid 40033900)
37. Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature, 463, 178-183.
38. Shoemaker, R.C., Schlueter, J. and Doyle, J.J. (2006) Paleopolyploidy and gene duplication in soybean and other legumes. Curr. Opin. Plant Biol., 9, 104-109. (Pubitemid 43292366)
39. Gurley, W.B., Hepburn, A.G. and Key, J.L. (1979) Sequence organization of the soybean genome. Biochim. Biophys. Acta, 561, 167-183.
40. Goldberg, R.B. (1978) DNA sequence organization in the soybean plant. Biochem. Genet., 16, 45-68. (Pubitemid 8300675)
41. Ohno, S. (1970) Evolution by Gene Duplication. Springer, Berlin.
42. Pickett, F.B. and Meeks-Wagner, D.R. (1995) Seeing double: appreciating genetic redundancy. Plant Cell, 7, 1347-1356.