Comparative analysis of base correlations in 5′ untranslated regions of various species

Gene

Volumn 375, Issue 1-2, 2006, Pages 80-86

  Osada, Yuko ^a   Saito, Rintaro ^a   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

Kozak consensus sequence; Mutual information; Shine Dalgarno sequence; Start codon; Translation initiation sites

Indexed keywords

DINUCLEOTIDE; NUCLEOTIDE;

5' UNTRANSLATED REGION; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; ENTROPY; EUKARYOTE; GENETIC CONSERVATION; GENETIC CORRELATION; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; SPECIES COMPARISON; TRANSCRIPTION INITIATION SITE; TRANSLATION INITIATION;

5' UNTRANSLATED REGIONS; BACTERIA; GENES, BACTERIAL; SPECIES SPECIFICITY;

EUKARYOTA; VERTEBRATA;

EID: 33744543456     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.02.018     Document Type: Article

References (33)

1. Ambrosini G., Praz V., Jagannathan V., and Bucher P. Signal search analysis server. Nucleic Acids Res. 31 (2003) 3618-3620
2. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212 (1990) 563-578
3. Chen H., Bjerknes M., Kumar R., and Jay E. Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res. 22 (1994) 4953-4957
4. de Smit M.H., and van Duin J. Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction. J. Mol. Biol. 235 (1994) 173-184
5. Durbin R., Eddy S.R., Krogh A., and Mitchison G.. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1999), Cambridge Univ. Press 260-298
6. Fuglsang A. Compositional nonrandomness upstream of start codons in archaebacteria. Gene 332 (2004) 89-95
7. Hagenbuchle O., Santer M., Steitz J.A., and Mans R.J. Conservation of the primary structure at the 3′ end of 18S rRNA from eucaryotic cells. Cell 13 (1978) 551-563
8. Hartz D., McPheeters D.S., and Gold L. Influence of mRNA determinants on translation initiation in Escherichia coli. J. Mol. Biol. 218 (1991) 83-97
9. Hatzigeorgiou A.G. Translation initiation start prediction in human cDNAs with high accuracy. Bioinformatics 18 (2002) 343-350
10. Kozak M. An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res. 15 (1987) 8125-8148
11. Kozak M. Adherence to the first-AUG rule when a second AUG codon follows closely upon the first. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 2662-2666
12. Kozak M. Initiation of translation in prokaryotes and eukaryotes. Gene 234 (1999) 187-208
13. Kozak M. Pushing the limits of the scanning mechanism for initiation of translation. Gene 299 (2002) 1-34
14. Lagunez-Otero J. rRNA-mRNA complementarity: implications for translation initiation. Trends Biochem. Sci. 18 (1993) 406-408
15. Mauro V.P., and Edelman G.M. rRNA-like sequences occur in diverse primary transcripts: implications for the control of gene expression. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 422-427
16. May E.E., Vouk M.A., Bitzer D.L., and Rosnick D.I. Coding theory based models for protein translation initiation in prokaryotic organisms. BioSystems 76 (2004) 249-260
17. Osada Y., Saito R., and Tomita M. Analysis of base-pairing potentials between 16S rRNA and 5′ UTR for translation initiation in various prokaryotes. Bioinformatics 15 (1999) 578-581
18. Ringquist S., et al. Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol. Microbiol. 6 (1992) 1219-1229
19. Salzberg S.L. A method for identifying splice sites and translational start sites in eukaryotic mRNA. Comput. Appl. Biosci. 13 (1997) 365-376
20. Sargan D.R., Gregory S.P., and Butterworth P.H. A possible novel interaction between the 3′-end of 18S ribosomal RNA and the 5′-leader sequence of many eukaryotic messenger RNAs. FEBS Lett. 147 (1982) 133-136
21. Sarge K.D., and Maxwell E.S. Evidence for a competitive-displacement model for the initiation of protein synthesis involving the intermolecular hybridization of 5S rRNA, 18S rRNA and mRNA. FEBS Lett. 294 (1991) 234-238
22. Schneider T.D. Information content of individual genetic sequences. J. Theor. Biol. 189 (1997) 427-441
23. Schneider T.D., Stormo G.D., Gold L., and Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188 (1986) 415-431
24. Schurr T., Nadir E., and Margalit H. Identification and characterization of E. coli ribosomal binding sites by free energy computation. Nucleic Acids Res. 21 (1993) 4019-4023
25. Shannon, C.E., 1948. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423, 623-656.
26. Shine J., and Dalgarno L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. U. S. A. 71 (1974) 1342-1346
27. Shultzaberger R.K., Bucheimer R.E., Rudd K.E., and Schneider T.D. Anatomy of Escherichia coli ribosome binding sites. J. Mol. Biol. 313 (2001) 215-228
28. Slupska M.M., King A.G., Fitz-Gibbon S., Besemer J., Borodovsky M., and Miller J.H. Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum. J. Mol. Biol. 309 (2001) 347-360
29. Stephens R.M., and Schneider T.D. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J. Mol. Biol. 228 4 (1992) 1124-1136
30. Stormo G.D. Information content and free energy in DNA-protein interactions. J. Theor. Biol. 195 (1998) 135-137
31. Tranque P., Hu M.C., Edelman G.M., and Mauro V.P. rRNA complementarity within mRNAs: a possible basis for mRNA-ribosome interactions and translational control. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 12238-12243
32. Verrier S.B., and Jean-Jean O. Complementarity between the mRNA 5′ untranslated region and 18S ribosomal RNA can inhibit translation. RNA 6 (2000) 584-597
33. Zien A., Ratsch G., Mika S., Scholkopf B., Lengauer T., and Muller K.R. Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics 16 (2000) 799-807