Ordered partitioning reveals extended splice-site consensus information

Genome Research

Volumn 14, Issue 1, 2004, Pages 67-78

  Weir, Michael ^a   Rice, Michael ^a  

^a WESLEYAN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BINDING SITE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA SPLICING; DNA STRUCTURE; DROSOPHILA; EXON; GENETIC CONSERVATION; GENETIC CORRELATION; GENETIC DATABASE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; SEQUENCE ANALYSIS; SPLICEOSOME;

ANIMALS; BASE PAIR MISMATCH; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; GENOME; MODELS, GENETIC; RNA SPLICE SITES;

EID: 0346505472     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1715204     Document Type: Article

References (44)

1. Aebi, M., Hornig, H., and Weissmann, C. 1987. 5′ cleavage site in eukaryotic pre-mRNA splicing is determined by the overall 5′ splice region, not by the conserved 5′ GU. Cell 50: 237-246.
2. Basharin, G.P. 1959. On a statistical estimate for the entropy of a sequence of independent random variables. Theor. Prob. Appl. 4: 333-336.
3. Burge, C.B., Tuschl, T., and Sharp, P.A. 1999. Splicing of precursors to mRNAs by the spliceosomes. In The RNA world (eds. R.F. Gesteland et al.), pp. 525-560. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
4. Burkard, M.E., Turner, D.H., and Tinoco, I. 1999. The interactions that shape RNA structure. In The RNA world (eds. R.F. Gesteland et al.), pp. 233-264. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
5. Chiara, M.D., Palandjian, L., Feld Kramer, R., and Reed, R. 1997. Evidence that U5 snRNP recognizes the 3′ splice site for catalytic step II in mammals. EMBO J. 16: 4746-4759.
6. Chua, K. and Reed, R. 2001. An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing. Mol. Cell. Biol. 21: 1509-1514.
7. Collins, C.A. and Guthrie, C. 1999. Allele-specific genetic interactions between Prp8 and RNA active site residues suggest a function for Prp8 at the catalytic core of the spliceosome. Genes & Dev. 13: 1970-1982.
8. Deshler, J.O. and Rossi, J.J. 1991. Unexpected point mutations activate cryptic 3′ splice sites by perturbing a natural secondary structure within a yeast intron. Genes & Dev. 5: 1252-1263.
9. Fields, C. 1990. Information content of Caenorhabditis elegans splice site sequences varies with intron length. Nucleic Acids Res. 18: 1509-1512.
10. Fouser, L.A. and Friesen, J.D. 1986. Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing. Cell 45: 81-93.
11. Goodall, G.J. and Filipowicz, W. 1991. Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants. EMBO J. 10: 2635-2644.
12. Guo, M. and Mount, S.M. 1995. Localization of sequences required for size-specific splicing of a small Drosophila intron in vitro. J. Mol. Biol. 253: 426-437.
13. Guo, M., Lo, P.C., and Mount, S.M. 1993. Species-specific signals for the splicing of a short Drosophila intron in vitro. Mol. Cell. Biol. 13: 1104-1118.
14. Hall, S.L. and Padgett, R.A. 1994. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J. Mol. Biol. 239: 357-365.
15. Hertel, K.J., Lynch, K.W., and Maniatis, T. 1997. Common themes in the function of transcription and splicing enhancers. Curr. Opin. Cell Biol. 9: 350-357.
16. Hertz, G.Z. and Stormo, G.D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
17. Lesser, C.F. and Guthrie, C. 1993. Mutations in U6 snRNA that alter splice site specificity: Implications for the active site. Science 262: 1982-1988.
18. Lim, L.P. and Burge, C.B. 2001. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. 98: 11193-11198.
19. Luukkonen, B.G. and Seraphin, B. 1998. Genetic interaction between U6 snRNA and the first intron nucleotide in Saccharomyces cerevisiae. RNA 4: 167-180.
20. Mount, S.M., Burks, C., Hertz, G., Stormo, G.D., White, O., and Fields, C. 1992. Splicing signals in Drosophila: Intron size, information content, and consensus sequences. Nucleic Acids Res. 20: 4255-4262.
21. Newman, A.J. and Norman, C. 1992. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68: 743-754.
22. Nilsen, T.W. 1998. RNA-RNA interactions in nuclear pre-mRNA splicing. In RNA structure and function (eds. R.W. Simons and M. Grunberg-Manago), pp. 279-307. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. Parker, R. and Guthrie, C. 1985. A point mutation in the conserved hexanucleotide at a yeast 5′ splice junction uncouples recognition, cleavage, and ligation. Cell 41: 107-118.
24. Patterson, B. and Guthrie, C. 1991. A U-rich tract enhances usage of an alternative 3′ splice site in yeast. Cell 64: 181-187.
25. Puig, O., Gottschalk, A., Fabrizio, P., and Seraphin, B. 1999. Interaction of the U1 snRNP with nonconserved intronic sequences affects 5′ splice site selection. Genes & Dev. 13: 569-580.
26. Reed, R. 2000. Mechanisms of fidelity in pre-mRNA splicing. Curr. Opin. Cell Biol. 12: 340-345.
27. Rosbash, M. and Seraphin, B. 1991. Who's on first? The U1 snRNP-5′ splice site interaction and splicing. Trends Biochem. Sci. 16: 187-190.
28. Rudner, D.Z., Kanaar, R., Breger, K.S., and Rio, D.C. 1996. Mutations in the small subunit of the Drosophila U2AF splicing factor cause lethality and developmental defects. Proc. Natl. Acad. Sci. 93: 10333-10337.
29. Schneider, T.D., Stormo, G.D., Gold, L., and Ehrenfeucht, A. 1986. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188: 415-431. [Schneider, T.D., Haemer, J.S., and Stormo, G.D. Appendix: Calculation of sampling uncertainty and variance.]
30. Shannon, C.E. and Weaver, W. 1949. The mathematical theory of communication. University of Illinois Press, Urbana, IL.
31. Siatecka, M., Reyes, J.L., and Konarska, M.M. 1999. Functional interactions of Prp8 with both splice sites at the spliceosomal catalytic center. Genes & Dev. 13: 1983-1993.
32. Siliciano, P.G. and Guthrie, C. 1988. 5′ splice site selection in yeast: Genetic alterations in base-pairing with U1 reveal additional requirements. Genes & Dev. 2: 1258-1267.
33. Sontheimer, E.J. and Steitz, J.A. 1993. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262: 1989-1996.
34. Spingola, M., Grate, L., Haussler, D., and Ares, M. 1999. Genome-wide bioinformatic and molecular analysis of yeast introns. RNA 5: 221-234.
35. Spradling, A.C., Stern, D.M., Kiss, I., Roote, J., Laverty, T., and Rubin, G.M. 1995. Gene disruptions using P transposable elements: An integral component of the Drosophila genome project. Proc. Natl. Acad. Sci. 92: 10824-10830.
36. Stapleton, M., Liao, G., Brokstein, P., Hong, L., Carninci, P., Shiraki, T., Hayashizaki, Y., Champe, M., Pacleb, J., Wan, K., et al. 2002. The Drosophila gene collection: Identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res. 12: 1294-1300.
37. Steitz, J.A. 1992. Splicing takes a holliday. Science 257: 888-889.
38. Stephens, R.M. and Schneider, T.D. 1992. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228: 1124-1136.
39. Vijayraghavan, U., Parker, R., Tamm, J., Iimura, Y., Rossi, J., Abelson, J., and Guthrie, C. 1986. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J. 5: 1683-1695.
40. Wu, S., Romfo, C.M., Nilsen, T.W., and Green, M.R. 1999. Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature 402: 832-835.
41. Yu, Y.-T., Scharl, E.C., Smith, C.M., and Steitz, J.A. 1999. The growing world of small nuclear ribonucleoproteins. In The RNA world (eds. R.F. Gesteland et al.), pp. 487-524. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
42. Zar, J.H. 1999. Biostatistical analysis, 4th ed. Prentice Hall, Upper Saddle River, NJ.
43. Zhang, D. and Rosbash, M. 1999. Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex. Genes & Dev. 13: 581-592.
44. Zorio, D.A. and Blumenthal, T. 1999. Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans. Nature 402: 835-838.