Genomewide comparative analysis of alternative splicing in plants

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 18, 2006, Pages 7175-7180

  Wang, Bing Bing ^a   Brendel, Volker ^a,b  

^a IOWA STATE UNIVERSITY   (United States)

^b Department of Statistics Center for Statistics and Applications in Forensic Evidence Iowa State University 2438 Osborn Dr Ames   (United States)

Author keywords

Conserved alternative splicing; Exon skipping; Intron retention; Non sense mediated decay; Spliced alignment

Indexed keywords

COMPLEMENTARY DNA;

ALTERNATIVE RNA SPLICING; ARABIDOPSIS; ARTICLE; DATA BASE; DNA DETERMINATION; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE FREQUENCY; GENE TARGETING; GENETIC CONSERVATION; GENOME ANALYSIS; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; RICE;

ALTERNATIVE SPLICING; ANIMALS; ARABIDOPSIS; DATABASES, NUCLEIC ACID; GENES, PLANT; GENOME, PLANT; HUMANS; INTERNET; INTRONS; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; SEQUENCE ANALYSIS, DNA;

ARABIDOPSIS; MAMMALIA;

EID: 33646484347     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0602039103     Document Type: Article

References (59)

1. Stamm, S., Ben-Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T. A. & Soreq, H. (2005) Gene 344, 1-20.
2. Lareau, L. F., Green, R. E., Bhatnagar, R. S. & Brenner, S. E. (2004) Curr. Opin. Struct. Biol. 14, 273-282.
3. Black, D. L. (2003) Annu. Rev. Kochern. 72, 291-336.
4. Gupta, S., Zink, D., Korn, B., Vingron, M. & Haas, S. A. (2004) Bioinformatics 20, 2579-2585.
5. Modrek, B., Resch, A., Grasso, C. & Lee, C. (2001) Nucleic Acids Res. 29, 2850-2859.
6. Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbruck, S., Krueger, S., Reich, J. & Bork, P. (2000) FEBS Lett. 474, 83-86.
7. Mironov, A. A., Fickett, J. W. & Gelfand, M. S. (1999) Genome Res. 9, 1288-1293.
8. Kan, Z., Rouchka, E. C., Gish, W. R. & States, D. J. (2001) Genome Res. 11, 889-900.
9. Brett, D., Pospisil, H., Valcarcel, J., Reich, J. & Bork, P. (2002) Nat. Genet. 30, 29-30.
10. Modrek, B. & Lee, C. (2002) Nat. Genet. 30, 13-19.
11. Lewis, B. P., Green, R. E. & Brenner, S. E. (2003) Proc. Natl. Acad. Sci. USA 100, 189-192.
12. Sorek, R., Shamir, R. & Ast, G. (2004) Trends Genet. 20, 68-71.
13. Pan, Q., Bakowski, M. A., Morris, Q., Zhang, W., Frey, B. J., Hughes, T. R. & Blencowe, B. J. (2005) Trends Genet. 21, 73-77.
14. Thanaraj, T. A., Clark, F. & Muilu, J. (2003) Nucleic Acids Res. 31, 2544-2552.
15. Sugnet, C. W., Kent, W. J., Ares, M., Jr. & Haussler, D. (2004) Pac. Symp. Biocomput. 9, 66-77.
16. Nurtdinov, R. N., Artamonova, I. I., Mironov, A. A. & Gelfand, M. S. (2003) Hum. Mol. Genet. 12, 1313-1320.
17. Yeo, G. W., Van Nostrand, E., Holste, D., Poggio, T. & Burge, C. B. (2005) Proc. Natl. Acad. Sci. USA 102, 2850-2855.
18. Lorkovic, Z. J., Wieczorek Kirk, D. A., Lambermon, M. H. & Filipowicz, W. (2000) Trends Plant Sci. 5, 160-167.
19. Reddy, A. S. N. (2001) Crit. Rev. Plant Sci. 20, 523-571.
20. Ko, C. H., Brendel, V., Taylor, R. D. & Walbot, V. (1998) Plant Mol. Biol. 36, 573-583.
21. Brown, J. W., Smith, P. & Simpson, C. G. (1996) Plant Mol. Biol. 32, 531-535.
22. Wang, B. B. & Brendel, V. (2004) Genome Biol. 5, R102.
23. Golovkin, M. & Reddy, A. S. (1996) Plant Cell 8, 1421-1435.
24. Lazar, G. & Goodman, H. M. (2000) Plant Mol. Biol. 42, 571-581.
25. Montag, K., Salamini, F. & Thompson, R. D. (1995) Nucleic Acids Res. 23, 2168-2177.
26. Macknight, R., Bancroft, I., Page, T., Lister, C., Schmidt, R., Love, K., Westphal, L., Murphy, G., Sherson, S., Cobbett, C., et al. (1997) Cell 89, 737-745.
27. Dinesh-Kumar, S. P. & Baker, B. J. (2000) Proc. Natl. Acad. Sci. USA 97, 1908-1913.
28. Werneke, J. M., Chatfield, J. M. & Ogren, W. L. (1989) Plant Cell 1, 815-825.
29. Baga, M., Glaze, S., Mallard, C. S. & Chibbar, R. N. (1999) Plant Mol. Biol. 40, 1019-1030.
30. Zhou, Y., Zhou, C., Ye, L., Dong, J., Xu, H., Cai, L., Zhang, L. & Wei, L. (2003) Genomics 82, 584-595.
31. Kazan, K. (2003) Trends Plant Sci. 8, 468-471.
32. Ner-Gaon, H., Halachmi, R., Savaldi-Goldstein, S., Rubin, E., Ophir, R. & Fluhr, R. (2004) Plant J. 39, 877-885.
33. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. & Shinozaki, K. (2004) Nucleic Acids Res. 32, 5096-5103.
34. Zhu, W., Schlueter, S. D. & Brendel, V. (2003) Plant Physiol. 132, 469-484.
35. Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith, R. K., Jr., Hannick, L. I., Maiti, R., Ronning, C. M., Rusch, D. B., Town, C. D., et al. (2003) Nucleic Acids Res. 31, 5654-5666.
36. Alexandrov, N. N., Troukhan, M. E., Brover, V. V., Tatarinova, T., Flavell, R. B. & Feldmann, K. A. (2006) Plant Mol. Biol. 60, 69-85.
37. Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M. & Gotoh, O. (2005) Gene 364, 53-62.
38. Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., et al. (2002) Nature 420, 316-320.
39. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., et al. (2002) Nature 420, 312-316.
40. Brendel, V., Xing, L. & Zhu, W. (2004) Bioinformatics 20, 1157-1169.
41. Sparks, M. E. & Brendel, V. (2005) Bioinformatics 21, Suppl. 3, iii20-iii30.
42. Yu, J., Wang, J., Lin, W., Li, S., Li, H., Zhou, J., Ni, P., Dong, W., Hu, S., Zeng, C., et al. (2005) PLoS Biol. 3, e38.
43. Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., et al. (2005) Plant Physiol. 138, 18-26.
44. Berget, S. M. (1995) J. Biol. Chem. 270, 2411-2414.
45. Nakai, K. & Sakamoto, H. (1994) Gene 141, 171-177.
46. Brown, J. W. (1996) Plant J. 10, 771-780.
47. Simpson, C. G., McQuade, C., Lyon, J. & Brown, J. W. (1998) Plant J. 15, 125-131.
48. Nagy, E. & Maquat, L. E. (1998) Trends Biochem. Sci. 23, 198-199.
49. Hori, K. & Watanabe, Y. (2005) Plant J. 43, 530-540.
50. Baker, K. E. & Parker, R. (2004) Curr. Opin. Cell Biol 16, 293-299.
51. Lejeune, F. & Maquat, L. E. (2005) Curr. Opin. Cell Biol. 17, 309-315.
52. Wollerton, M. C., Gooding, C., Wagner, E. J., Garcia-Blanco, M. A. & Smith, C. W. (2004) Mol. Cell 13, 91-100.
53. Haas, B. J., Volfovsky, N., Town, C. D., Troukhan, M., Alexandrov, N., Feldmann, K. A., Flavell, R. B., White, O. & Salzberg, S. L. (2002) Genome Biol. 3, RESEARCH0029.
54. Deutsch, M. & Long, M. (1999) Nucleic Acids Res. 27, 3219-3228.
55. Lim, L. P. & Burge, C. B. (2001) Proc. Natl. Acad. Sci. USA 98, 11193-11198.
56. Kornblihtt, A. R. (2005) Curr. Opin. Cell Biol. 17, 262-268.
57. Dong, Q., Schlueter, S. D. & Brendel, V. (2004) Nucleic Acids Res. 32, D354-D359.
58. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., et al. (2002) Nature 420, 563-573.
59. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.