메뉴 건너뛰기




Volumn 32, Issue 5, 2004, Pages 1774-1782

Comparative analysis of orthologous eukaryotic mRNAs: Potential hidden functional signals

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 3042668591     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh313     Document Type: Article
Times cited : (77)

References (60)
  • 5
    • 0027280998 scopus 로고
    • Strong conservation of non-coding sequences during vertebrates evolution: Potential involvement in post-transcriptional regulation of gene expression
    • Duret,L., Dorkeld,F. and Gautier,C. (1993) Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res., 21, 2315-2322.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 2315-2322
    • Duret, L.1    Dorkeld, F.2    Gautier, C.3
  • 6
    • 0030748996 scopus 로고    scopus 로고
    • Making (anti)sense of non-coding sequence conservation
    • Lipman,D.J. (1997) Making (anti)sense of non-coding sequence conservation. Nucleic Acids Res., 25, 3580-3583.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3580-3583
    • Lipman, D.J.1
  • 7
    • 0032848247 scopus 로고    scopus 로고
    • Pattern of selective constraint in C. elegans and C. briggsae genomes
    • Shabalina,S.A. and Kondrashov,A.S. (1999) Pattern of selective constraint in C. elegans and C. briggsae genomes. Genet. Res., 74, 23-30.
    • (1999) Genet. Res. , vol.74 , pp. 23-30
    • Shabalina, S.A.1    Kondrashov, A.S.2
  • 10
    • 0035802386 scopus 로고    scopus 로고
    • Structural and functional features of eukaryotic mRNA untranslated regions
    • Pesole,G., Mignone,F., Gissi,C., Grillo,G., Licciulli,F. and Liuni,S. (2001) Structural and functional features of eukaryotic mRNA untranslated regions. Gene, 276, 73-81.
    • (2001) Gene , vol.276 , pp. 73-81
    • Pesole, G.1    Mignone, F.2    Gissi, C.3    Grillo, G.4    Licciulli, F.5    Liuni, S.6
  • 11
    • 0035984473 scopus 로고    scopus 로고
    • Evolutionary dynamics of mammalian mRNA untranslated regions by comparative analysis of orthologous human, artiodactyl and rodent gene pairs
    • Larizza,A., Makalowski,W., Pesole,G. and Saccone,C. (2002) Evolutionary dynamics of mammalian mRNA untranslated regions by comparative analysis of orthologous human, artiodactyl and rodent gene pairs. Comput. Chem., 26, 479-490.
    • (2002) Comput. Chem. , vol.26 , pp. 479-490
    • Larizza, A.1    Makalowski, W.2    Pesole, G.3    Saccone, C.4
  • 12
    • 0030927867 scopus 로고    scopus 로고
    • Searching for regulatory elements in human noncoding sequences
    • Duret,L. and Bucher,P. (1997) Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol., 7, 399-406.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 399-406
    • Duret, L.1    Bucher, P.2
  • 17
    • 2242441596 scopus 로고    scopus 로고
    • The context organization of functional regions in yeast genes with high-level expression
    • Kochetov,A.V., Sarai,A., Vorob'ev,D.G. and Kolchanov,N.A. (2002) [The context organization of functional regions in yeast genes with high-level expression]. Mol. Biol. (Mosk.), 36, 1026-1034.
    • (2002) Mol. Biol. (Mosk.) , vol.36 , pp. 1026-1034
    • Kochetov, A.V.1    Sarai, A.2    Vorob'ev, D.G.3    Kolchanov, N.A.4
  • 18
    • 0024546509 scopus 로고
    • The scanning model for translation: An update
    • Kozak,M. (1989) The scanning model for translation: an update. J. Cell Biol., 108, 229-241.
    • (1989) J. Cell Biol. , vol.108 , pp. 229-241
    • Kozak, M.1
  • 20
    • 0033061571 scopus 로고    scopus 로고
    • Initiation of translation in prokaryotes and eukaryotes
    • Kozak,M. (1999) Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.
    • (1999) Gene , vol.234 , pp. 187-208
    • Kozak, M.1
  • 21
    • 0037121050 scopus 로고    scopus 로고
    • Pushing the limits of the scanning mechanism for initiation of translation
    • Kozak,M. (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene, 299, 1-34.
    • (2002) Gene , vol.299 , pp. 1-34
    • Kozak, M.1
  • 22
    • 0027452550 scopus 로고
    • Regulating the fate of mRNA: The control of cellular iron metabolism
    • Klausner,R.D., Rouault,T.A. and Harford,J.B. (1993) Regulating the fate of mRNA: the control of cellular iron metabolism. Cell, 72, 19-28.
    • (1993) Cell , vol.72 , pp. 19-28
    • Klausner, R.D.1    Rouault, T.A.2    Harford, J.B.3
  • 23
    • 0034459468 scopus 로고    scopus 로고
    • Upstream open reading frames as regulators of mRNA translation
    • Morris,D.R. and Geballe,A.P. (2000) Upstream open reading frames as regulators of mRNA translation. Mol. Cell. Biol., 20, 8635-8642.
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 8635-8642
    • Morris, D.R.1    Geballe, A.P.2
  • 24
    • 0035396727 scopus 로고    scopus 로고
    • Internal ribosome entry sites in eukaryotic mRNA molecules
    • Hellen,C.U. and Sarnow,P. (2001) Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev., 15, 1593-1612.
    • (2001) Genes Dev. , vol.15 , pp. 1593-1612
    • Hellen, C.U.1    Sarnow, P.2
  • 25
    • 0037308625 scopus 로고    scopus 로고
    • Translational control by the 3′-UTR: The ends specify the means
    • Mazumder,B., Seshadri,V. and Fox,P.L. (2003) Translational control by the 3′-UTR: the ends specify the means. Trends Biochem. Sci., 28, 91-98.
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 91-98
    • Mazumder, B.1    Seshadri, V.2    Fox, P.L.3
  • 26
    • 0035137890 scopus 로고    scopus 로고
    • Endless possibilities: Translation termination and stop codon recognition
    • Bertram,G., Innes,S., Minella,O., Richardson,J. and Stansfield,I. (2001) Endless possibilities: translation termination and stop codon recognition. Microbiology, 147, 255-269.
    • (2001) Microbiology , vol.147 , pp. 255-269
    • Bertram, G.1    Innes, S.2    Minella, O.3    Richardson, J.4    Stansfield, I.5
  • 27
    • 0037310005 scopus 로고    scopus 로고
    • Making sense of mimic in translation termination
    • Nakamura,Y. and Ito,K. (2003) Making sense of mimic in translation termination. Trends Biochem. Sci., 28, 99-105.
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 99-105
    • Nakamura, Y.1    Ito, G.K.2
  • 28
    • 0037439231 scopus 로고    scopus 로고
    • Termination of translation: Interplay of mRNA, rRNAs and release factors?
    • Kisselev,L., Ehrenberg,M. and Frolova,L. (2003) Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO J., 22, 175-182.
    • (2003) EMBO J. , vol.22 , pp. 175-182
    • Kisselev, L.1    Ehrenberg, M.2    Frolova, L.3
  • 29
    • 0029153552 scopus 로고
    • The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae
    • Bonetti,B., Fu,L., Moon,J. and Bedwell,D.M. (1995) The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol., 251, 334-345.
    • (1995) J. Mol. Biol. , vol.251 , pp. 334-345
    • Bonetti, B.1    Fu, L.2    Moon, J.3    Bedwell, D.M.4
  • 30
    • 0029047851 scopus 로고
    • Translational termination efficiency in mammals is influenced by the base following the stop codon
    • McCaughan,K.K., Brown,C.M., Dalphin,M.E., Berry,M.J. and Tate,W.P. (1995) Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc. Natl Acad. Sci. USA, 92, 5431-5435.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 5431-5435
    • McCaughan, K.K.1    Brown, C.M.2    Dalphin, M.E.3    Berry, M.J.4    Tate, W.P.5
  • 32
    • 12644303224 scopus 로고    scopus 로고
    • Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G
    • Tarun,S.Z.,Jr and Sachs,A.B. (1996) Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. EMBO J., 15, 7168-7177.
    • (1996) EMBO J. , vol.15 , pp. 7168-7177
    • Tarun Jr., S.Z.1    Sachs, A.B.2
  • 33
    • 0032112017 scopus 로고    scopus 로고
    • Circularization of mRNA by eukaryotic translation initiation factors
    • Wells,S.E., Hillner,P.E., Vale,R.D. and Sachs,A.B. (1998) Circularization of mRNA by eukaryotic translation initiation factors. Mol. Cell, 2, 135-140.
    • (1998) Mol. Cell , vol.2 , pp. 135-140
    • Wells, S.E.1    Hillner, P.E.2    Vale, R.D.3    Sachs, A.B.4
  • 34
    • 0033059981 scopus 로고    scopus 로고
    • Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation and interrelationships with other steps in mRNA synthesis
    • Zhao,J., Hyman,L. and Moore,C. (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev., 63, 405-445.
    • (1999) Microbiol. Mol. Biol. Rev. , vol.63 , pp. 405-445
    • Zhao, J.1    Hyman, L.2    Moore, C.3
  • 35
    • 0033788228 scopus 로고    scopus 로고
    • The ends of the affair: Capping and polyadenylation
    • Shatkin,A.J. and Manley,J.L. (2000) The ends of the affair: capping and polyadenylation. Nature Struct. Biol., 7, 838-842.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 838-842
    • Shatkin, A.J.1    Manley, J.L.2
  • 36
    • 0037164730 scopus 로고    scopus 로고
    • Polyadenylation: A tail of two complexes
    • Proudfoot,N. and O'Sullivan,J. (2002) Polyadenylation: a tail of two complexes. Curr. Biol., 12, R855-R857.
    • (2002) Curr. Biol. , vol.12
    • Proudfoot, N.1    O'Sullivan, J.2
  • 37
    • 0017089669 scopus 로고
    • 3′ non-coding region sequences in eukaryotic messenger RNA
    • Proudfoot,N.J. and Brownlee,G.G. (1976) 3′ non-coding region sequences in eukaryotic messenger RNA. Nature, 263, 211-214.
    • (1976) Nature , vol.263 , pp. 211-214
    • Proudfoot, N.J.1    Brownlee, G.G.2
  • 38
    • 0037171440 scopus 로고    scopus 로고
    • Reexamining the polyadenylation signal: Were we wrong about AAUAAA?
    • MacDonald,C.C. and Redondo,J.L. (2002) Reexamining the polyadenylation signal: were we wrong about AAUAAA? Mol. Cell. Endocrinol., 190, 1-8.
    • (2002) Mol. Cell. Endocrinol. , vol.190 , pp. 1-8
    • MacDonald, C.C.1    Redondo, J.L.2
  • 39
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis,M., Patterson,N., Endrizzi,M., Birren,B. and Lander,E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 43
    • 0344875191 scopus 로고    scopus 로고
    • Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3′UTRs
    • Shabalina,S.A., Ogurtsov,A.Y., Lipman,D.J. and Kondrashov,A.S. (2003) Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3′UTRs. Nucleic Acids Res., 31, 5433-5439.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5433-5439
    • Shabalina, S.A.1    Ogurtsov, A.Y.2    Lipman, D.J.3    Kondrashov, A.S.4
  • 44
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 45
    • 0342947190 scopus 로고
    • Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons
    • Kimura,M. (1981) Possibility of extensive neutral evolution under stabilizing selection with special reference to nonrandom usage of synonymous codons. Proc. Natl Acad. Sci. USA, 78, 5773-5777.
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 5773-5777
    • Kimura, M.1
  • 46
    • 0032483028 scopus 로고    scopus 로고
    • Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences
    • Makalowski,W. and Boguski,M.S. (1998) Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl Acad. Sci. USA, 95, 9407-9412.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9407-9412
    • Makalowski, W.1    Boguski, M.S.2
  • 47
    • 0031856647 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes
    • Makalowski,W. and Boguski,M.S. (1998) Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes. J. Mol. Evol., 47, 119-121.
    • (1998) J. Mol. Evol. , vol.47 , pp. 119-121
    • Makalowski, W.1    Boguski, M.S.2
  • 49
    • 0037380022 scopus 로고    scopus 로고
    • Transcription-associated mutational asymmetry in mammalian evolution
    • Green,P., Ewing,B., Miller,W., Thomas,P.J. and Green,E.D. (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nature Genet., 33, 514-517.
    • (2003) Nature Genet. , vol.33 , pp. 514-517
    • Green, P.1    Ewing, B.2    Miller, W.3    Thomas, P.J.4    Green, E.D.5
  • 51
  • 52
    • 0034117544 scopus 로고    scopus 로고
    • Two classes of genes in plants
    • Carels,N. and Bernardi,G. (2000) Two classes of genes in plants. Genetics, 154, 1819-1825.
    • (2000) Genetics , vol.154 , pp. 1819-1825
    • Carels, N.1    Bernardi, G.2
  • 53
    • 0242290126 scopus 로고    scopus 로고
    • The influence of translational selection on codon usage in fishes from the family Cyprinidae
    • Romero,H., Zavala,A., Musto,H. and Bernardi,G. (2003) The influence of translational selection on codon usage in fishes from the family Cyprinidae. Gene, 317, 141-147.
    • (2003) Gene , vol.317 , pp. 141-147
    • Romero, H.1    Zavala, A.2    Musto, H.3    Bernardi, G.4
  • 54
    • 0036133146 scopus 로고    scopus 로고
    • Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents
    • Konu,O. and Li,M.D. (2002) Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. J. Mol. Evol., 54, 35-41.
    • (2002) J. Mol. Evol. , vol.54 , pp. 35-41
    • Konu, O.1    Li, M.D.2
  • 55
    • 0141854009 scopus 로고    scopus 로고
    • The human transcriptome map reveals extremes in gene density, intron length, GC content and repeat pattern for domains of highly and weakly expressed genes
    • Versteeg,R., van Schaik,B.D., van Batenburg,M.F., Roos,M., Monajemi,R., Caron,H., Bussemaker,H.J. and van Kampen,A.H. (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content and repeat pattern for domains of highly and weakly expressed genes. Genome Res., 13, 1998-2004.
    • (2003) Genome Res. , vol.13 , pp. 1998-2004
    • Versteeg, R.1    van Schaik, B.D.2    van Batenburg, M.F.3    Roos, M.4    Monajemi, R.5    Caron, H.6    Bussemaker, H.J.7    van Kampen, A.H.8
  • 56
    • 0028012044 scopus 로고
    • Effect of sequence context at stop codons on efficiency of reinitiation in GCN4 translational control
    • Grant,C.M. and Hinnebusch,A.G. (1994) Effect of sequence context at stop codons on efficiency of reinitiation in GCN4 translational control. Mol. Cell. Biol., 14, 606-618.
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 606-618
    • Grant, C.M.1    Hinnebusch, A.G.2
  • 57
    • 0032029584 scopus 로고    scopus 로고
    • The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability
    • Vilela,C., Linz,B., Rodrigues-Pousada,C. and McCarthy,J.E. (1998) The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability. Nucleic Acids Res., 26, 1150-1159.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1150-1159
    • Vilela, C.1    Linz, B.2    Rodrigues-Pousada, C.3    McCarthy, J.E.4
  • 58
    • 0030803256 scopus 로고    scopus 로고
    • Translational regulation of yeast GCN4. A window on factors that control initiator-trna binding to the ribosome
    • Hinnebusch,A.G. (1997) Translational regulation of yeast GCN4. A window on factors that control initiator-trna binding to the ribosome. J. Biol. Chem., 272, 21661-21664.
    • (1997) J. Biol. Chem. , vol.272 , pp. 21661-21664
    • Hinnebusch, A.G.1
  • 59
    • 0034065158 scopus 로고    scopus 로고
    • The structure and function of initiation factors in eukaryotic protein synthesis
    • Pestova,T.V. and Hellen,C.U. (2000) The structure and function of initiation factors in eukaryotic protein synthesis. Cell. Mol. Life Sci., 57, 651-674.
    • (2000) Cell. Mol. Life Sci. , vol.57 , pp. 651-674
    • Pestova, T.V.1    Hellen, C.U.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.