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Volumn 10, Issue 1, 2010, Pages

Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

Author keywords

[No Author keywords available]

Indexed keywords

CILIATE; DNA; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOMICS; PHYLOGENETICS;

EID: 77952840944     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-129     Document Type: Article
Times cited : (3)

References (43)
  • 1
    • 0032560007 scopus 로고    scopus 로고
    • A highly conserved RNA-binding protein for cytoplasmic mRNA localization in vertebrates
    • 10.1016/S0960-9822(98)70200-3. 9560341
    • A highly conserved RNA-binding protein for cytoplasmic mRNA localization in vertebrates. JO Deshler MI Highett T Abramson BJ Schnapp, Curr Biol 1998 8 9 489 496 10.1016/S0960-9822(98)70200-3 9560341
    • (1998) Curr Biol , vol.8 , Issue.9 , pp. 489-496
    • Deshler, J.O.1    Highett, M.I.2    Abramson, T.3    Schnapp, B.J.4
  • 2
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    • 10.1038/nature03441. 15735639
    • Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. X Xie J Lu EJ Kulbokas TR Golub V Mootha K Lindblad-Toh ES Lander M Kellis, Nature 2005 434 7031 338 345 10.1038/nature03441 15735639
    • (2005) Nature , vol.434 , Issue.7031 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 3
    • 33645217973 scopus 로고    scopus 로고
    • Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster
    • 10.1073/pnas.0509260103. 16537387
    • Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. AP Gerber S Luschnig MA Krasnow PO Brown D Herschlag, Proc Natl Acad Sci USA 2006 103 12 4487 4492 10.1073/pnas.0509260103 16537387
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.12 , pp. 4487-4492
    • Gerber, A.P.1    Luschnig, S.2    Krasnow, M.A.3    Brown, P.O.4    Herschlag, D.5
  • 4
    • 0031767514 scopus 로고    scopus 로고
    • The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts
    • 9735368
    • The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. EC Lai C Burks JW Posakony, Development 1998 125 20 4077 4088 9735368
    • (1998) Development , vol.125 , Issue.20 , pp. 4077-4088
    • Lai, E.C.1    Burks, C.2    Posakony, J.W.3
  • 5
    • 0032909883 scopus 로고    scopus 로고
    • A highly conserved sequence in the 3'- untranslated region of the Drosophila Adh gene plays a functional role in Adh expression
    • 9927459
    • A highly conserved sequence in the 3'- untranslated region of the Drosophila Adh gene plays a functional role in Adh expression. J Parsch W Stephan S Tanda, Genetics 1999 151 2 667 674 9927459
    • (1999) Genetics , vol.151 , Issue.2 , pp. 667-674
    • Parsch, J.1    Stephan, W.2    Tanda, S.3
  • 6
    • 55449121696 scopus 로고    scopus 로고
    • Revealing posttranscriptional regulatory elements through network-level conservation
    • 10.1371/journal.pcbi.0010069. 16355253
    • Revealing posttranscriptional regulatory elements through network-level conservation. CS Chan O Elemento S Tavazoie, PLoS Comput Biol 2005 1 7 69 10.1371/journal.pcbi.0010069 16355253
    • (2005) PLoS Comput Biol , vol.1 , Issue.7 , pp. 569
    • Chan, C.S.1    Elemento, O.2    Tavazoie, S.3
  • 7
    • 33749251416 scopus 로고    scopus 로고
    • A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes
    • 10.1261/rna.51306. 16917125
    • A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes. A Hajarnavis R Durbin, RNA 2006 12 10 1786 1789 10.1261/rna.51306 16917125
    • (2006) RNA , vol.12 , Issue.10 , pp. 1786-1789
    • Hajarnavis, A.1    Durbin, R.2
  • 8
    • 34548093996 scopus 로고    scopus 로고
    • A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs
    • 10.1186/gb-2005-6-10-r86. 16207357
    • A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. R Shalgi M Lapidot R Shamir Y Pilpel, Genome Biol 2005 6 10 86 10.1186/gb-2005-6-10-r86 16207357
    • (2005) Genome Biol , vol.6 , Issue.10 , pp. 1886
    • Shalgi, R.1    Lapidot, M.2    Shamir, R.3    Pilpel, Y.4
  • 9
    • 0028930788 scopus 로고
    • An AU-rich element in the 3' untranslated region of the spinach chloroplast petD gene participates in sequence-specific RNA-protein complex formation
    • 7891696
    • An AU-rich element in the 3' untranslated region of the spinach chloroplast petD gene participates in sequence-specific RNA-protein complex formation. Q Chen CC Adams L Usack J Yang RA Monde DB Stern, Mol Cell Biol 1995 15 4 2010 2018 7891696
    • (1995) Mol Cell Biol , vol.15 , Issue.4 , pp. 2010-2018
    • Chen, Q.1    Adams, C.C.2    Usack, L.3    Yang, J.4    Monde, R.A.5    Stern, D.B.6
  • 10
    • 34247562405 scopus 로고    scopus 로고
    • Regions in the 3' untranslated region confer stage-specific expression to the Leishmania mexicana a600 -4 gene
    • 10.1016/j.molbiopara.2007.02.010. 17433460
    • Regions in the 3' untranslated region confer stage-specific expression to the Leishmania mexicana a600 -4 gene. A Murray C Fu G Habibi WR McMaster, Mol Biochem Parasitol 2007 153 2 125 132 10.1016/j.molbiopara.2007.02.010 17433460
    • (2007) Mol Biochem Parasitol , vol.153 , Issue.2 , pp. 125-132
    • Murray, A.1    Fu, C.2    Habibi, G.3    McMaster, W.R.4
  • 11
    • 50549098379 scopus 로고    scopus 로고
    • Discovering regulatory motifs in the Plasmodium genome using comparative genomics
    • 10.1093/bioinformatics/btn348. 18611947
    • Discovering regulatory motifs in the Plasmodium genome using comparative genomics. J Wu DH Sieglaff J Gervin XS Xie, Bioinformatics 2008 24 17 1843 1849 10.1093/bioinformatics/btn348 18611947
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1843-1849
    • Wu, J.1    Sieglaff, D.H.2    Gervin, J.3    Xie, X.S.4
  • 13
    • 55949128866 scopus 로고    scopus 로고
    • Prediction of human miRNAs using tissue-selective motifs in 3' UTRs
    • 10.1073/pnas.0809151105. 18952845
    • Prediction of human miRNAs using tissue-selective motifs in 3' UTRs. YM Chang HF Juan TY Lee YY Chang YM Yeh WH Li AC Shih, Proc Natl Acad Sci USA 2008 105 44 17061 17066 10.1073/pnas.0809151105 18952845
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.44 , pp. 17061-17066
    • Chang, Y.M.1    Juan, H.F.2    Lee, T.Y.3    Chang, Y.Y.4    Yeh, Y.M.5    Li, W.H.6    Shih, A.C.7
  • 14
    • 58449122276 scopus 로고    scopus 로고
    • Genetic diversity in the Paramecium aurelia species complex
    • 10.1093/molbev/msn266. 19023087
    • Genetic diversity in the Paramecium aurelia species complex. F Catania F Wurmser AA Potekhin E Przybos M Lynch, Mol Biol Evol 2009 26 2 421 431 10.1093/molbev/msn266 19023087
    • (2009) Mol Biol Evol , vol.26 , Issue.2 , pp. 421-431
    • Catania, F.1    Wurmser, F.2    Potekhin, A.A.3    Przybos, E.4    Lynch, M.5
  • 15
    • 34547571030 scopus 로고    scopus 로고
    • G:Profiler - A web-based toolset for functional profiling of gene lists from large-scale experiments
    • 10.1093/nar/gkm226. 17478515
    • g:Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. J Reimand M Kull H Peterson J Hansen J Vilo, Nucleic Acids Res 2007 35 Web Server 193 200 10.1093/nar/gkm226 17478515
    • (2007) Nucleic Acids Res , Issue.WEB SERVER , pp. 23193-200
    • Reimand, J.1    Kull, M.2    Peterson, H.3    Hansen, J.4    Vilo, J.5
  • 16
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: A web-based software toolkit for Gene Ontology enrichment analysis
    • 10.1093/nar/gkn276. 18487275
    • GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Q Zheng XJ Wang, Nucleic Acids Res 2008 36 Web Server 358 363 10.1093/nar/gkn276 18487275
    • (2008) Nucleic Acids Res , Issue.WEB SERVER , pp. 23358-363
    • Zheng, Q.1    Wang, X.J.2
  • 17
    • 84985161094 scopus 로고
    • Paramecium-Sonneborni N -Sp, a New Member of the Paramecium-Aurelia Species -Complex
    • Paramecium-Sonneborni N -Sp, a New Member of the Paramecium-Aurelia Species -Complex. KJ Aufderheide PM Daggett TA Nerad, Journal of Protozoology 1983 30 1 128 131
    • (1983) Journal of Protozoology , vol.30 , Issue.1 , pp. 128-131
    • Aufderheide, K.J.1    Daggett, P.M.2    Nerad, T.A.3
  • 18
    • 0000448959 scopus 로고
    • The paramecium-aurelia complex of 14 sibling species
    • 10.2307/3224977
    • The Paramecium-Aurelia Complex of 14 Sibling Species. TM Sonneborn, Transactions of the American Microscopical Society 1975 94 2 155 178 10.2307/3224977
    • (1975) Transactions of the American Microscopical Society , vol.94 , Issue.2 , pp. 155-178
    • Sonneborn, T.M.1
  • 19
    • 67449088149 scopus 로고    scopus 로고
    • Large-scale genome analysis reveals unique features of microRNAs
    • 10.1016/j.gene.2009.04.027. 19422892
    • Large-scale genome analysis reveals unique features of microRNAs. B Zhang EJ Stellwag X Pan, Gene 2009 443 1-2 100 109 10.1016/j.gene.2009.04.027 19422892
    • (2009) Gene , vol.443 , Issue.1-2 , pp. 100-109
    • Zhang, B.1    Stellwag, E.J.2    Pan, X.3
  • 20
  • 22
    • 30744468557 scopus 로고    scopus 로고
    • Evidence that miRNAs are different from other RNAs
    • 10.1007/s00018-005-5467-7. 16395542
    • Evidence that miRNAs are different from other RNAs. BH Zhang XP Pan SB Cox GP Cobb TA Anderson, Cell Mol Life Sci 2006 63 2 246 254 10.1007/s00018-005-5467-7 16395542
    • (2006) Cell Mol Life Sci , vol.63 , Issue.2 , pp. 246-254
    • Zhang, B.H.1    Pan, X.P.2    Cox, S.B.3    Cobb, G.P.4    Anderson, T.A.5
  • 23
    • 34347406537 scopus 로고    scopus 로고
    • Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions
    • 10.1186/1471-2105-8-174. 17524134
    • Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions. D Cora F Di Cunto M Caselle P Provero, BMC Bioinformatics 2007 8 174 10.1186/1471-2105-8-174 17524134
    • (2007) BMC Bioinformatics , vol.8 , pp. 174
    • Cora, D.1    Di Cunto, F.2    Caselle, M.3    Provero, P.4
  • 25
    • 46249100442 scopus 로고    scopus 로고
    • Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
    • 10.1186/gb-2008-9-1-r22. 18226245
    • Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. A Ivan MS Halfon S Sinha, Genome Biol 2008 9 1 22 10.1186/gb-2008-9-1-r22 18226245
    • (2008) Genome Biol , vol.9 , Issue.1 , pp. 1822
    • Ivan, A.1    Halfon, M.S.2    Sinha, S.3
  • 26
    • 39149108478 scopus 로고    scopus 로고
    • Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila
    • 10.1186/1471-2105-8-432. 17996040
    • Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila. J Gu H Fu X Zhang Y Li, BMC Bioinformatics 2007 8 432 10.1186/1471-2105-8-432 17996040
    • (2007) BMC Bioinformatics , vol.8 , pp. 432
    • Gu, J.1    Fu, H.2    Zhang, X.3    Li, Y.4
  • 27
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin -4 encodes small RNAs with antisense complementarity to lin-14
    • 10.1016/0092-8674(93)90529-Y. 8252621
    • The C. elegans heterochronic gene lin -4 encodes small RNAs with antisense complementarity to lin-14. RC Lee RL Feinbaum V Ambros, Cell 1993 75 5 843 854 10.1016/0092-8674(93)90529-Y 8252621
    • (1993) Cell , vol.75 , Issue.5 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 28
    • 0027730383 scopus 로고
    • Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans
    • 10.1016/0092-8674(93)90530-4. 8252622
    • Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. B Wightman I Ha G Ruvkun, Cell 1993 75 5 855 862 10.1016/0092-8674(93)90530-4 8252622
    • (1993) Cell , vol.75 , Issue.5 , pp. 855-862
    • Wightman, B.1    Ha, I.2    Ruvkun, G.3
  • 29
    • 0037162702 scopus 로고    scopus 로고
    • Prediction of plant microRNA targets
    • 10.1016/S0092-8674(02)00863-2. 12202040
    • Prediction of plant microRNA targets. MW Rhoades BJ Reinhart LP Lim CB Burge B Bartel DP Bartel, Cell 2002 110 4 513 520 10.1016/S0092-8674(02)00863-2 12202040
    • (2002) Cell , vol.110 , Issue.4 , pp. 513-520
    • Rhoades, M.W.1    Reinhart, B.J.2    Lim, L.P.3    Burge, C.B.4    Bartel, B.5    Bartel, D.P.6
  • 31
    • 0032247826 scopus 로고    scopus 로고
    • Protein coding gene trees in ciliates: Comparison with rRNA-based phylogenies
    • 10.1006/mpev.1998.0534. 10051383
    • Protein coding gene trees in ciliates: comparison with rRNA-based phylogenies. AB Tourancheau E Villalobo N Tsao A Torres RE Pearlman, Mol Phylogenet Evol 1998 10 3 299 309 10.1006/mpev.1998.0534 10051383
    • (1998) Mol Phylogenet Evol , vol.10 , Issue.3 , pp. 299-309
    • Tourancheau, A.B.1    Villalobo, E.2    Tsao, N.3    Torres, A.4    Pearlman, R.E.5
  • 32
    • 65349158393 scopus 로고    scopus 로고
    • Differential retention of metabolic genes following whole-genome duplication
    • 10.1093/molbev/msp026. 19218282
    • Differential retention of metabolic genes following whole-genome duplication. JF Gout L Duret D Kahn, Mol Biol Evol 2009 26 5 1067 1072 10.1093/molbev/msp026 19218282
    • (2009) Mol Biol Evol , vol.26 , Issue.5 , pp. 1067-1072
    • Gout, J.F.1    Duret, L.2    Kahn, D.3
  • 33
    • 19344365947 scopus 로고    scopus 로고
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    • 10.1371/journal.pbio.0020079. 15024427
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. AP Gerber D Herschlag PO Brown, PLoS Biol 2004 2 3 79 10.1371/journal.pbio.0020079 15024427
    • (2004) PLoS Biol , vol.2 , Issue.3 , pp. 579
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 34
    • 0041327747 scopus 로고    scopus 로고
    • Variations in yeast 3'-processing cis-elements correlate with transcript stability
    • 10.1016/S0168-9525(03)00196-3. 12957538
    • Variations in yeast 3'-processing cis-elements correlate with transcript stability. JH Graber, Trends Genet 2003 19 9 473 476 10.1016/S0168-9525(03) 00196-3 12957538
    • (2003) Trends Genet , vol.19 , Issue.9 , pp. 473-476
    • Graber, J.H.1
  • 35
    • 44849120634 scopus 로고    scopus 로고
    • Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia
    • 10.1101/gad.473008. 18519642
    • Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. G Lepere M Betermier E Meyer S Duharcourt, Genes Dev 2008 22 11 1501 1512 10.1101/gad.473008 18519642
    • (2008) Genes Dev , vol.22 , Issue.11 , pp. 1501-1512
    • Lepere, G.1    Betermier, M.2    Meyer, E.3    Duharcourt, S.4
  • 36
    • 63349109487 scopus 로고    scopus 로고
    • Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia
    • 10.1093/nar/gkn1018. 19103667
    • Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia. G Lepere M Nowacki V Serrano JF Gout G Guglielmi S Duharcourt E Meyer, Nucleic Acids Res 2009 37 3 903 915 10.1093/nar/gkn1018 19103667
    • (2009) Nucleic Acids Res , vol.37 , Issue.3 , pp. 903-915
    • Lepere, G.1    Nowacki, M.2    Serrano, V.3    Gout, J.F.4    Guglielmi, G.5    Duharcourt, S.6    Meyer, E.7
  • 37
    • 33846079515 scopus 로고    scopus 로고
    • ParameciumDB: A community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
    • 10.1093/nar/gkl777. 17142227
    • ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. O Arnaiz S Cain J Cohen L Sperling, Nucleic Acids Res 2007 35 Database 439 444 10.1093/nar/gkl777 17142227
    • (2007) Nucleic Acids Res , Issue.DATABASE , pp. 4439-444
    • Arnaiz, O.1    Cain, S.2    Cohen, J.3    Sperling, L.4
  • 39
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • 10.1007/BF00993379
    • Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization. TL Bailey C Elkan, Machine Learning 1995 21 1-2 51 80 10.1007/BF00993379
    • (1995) Machine Learning , vol.21 , Issue.1-2 , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2
  • 40
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: A sequence logo generator
    • 10.1101/gr.849004. 15173120
    • WebLogo: a sequence logo generator. GE Crooks G Hon JM Chandonia SE Brenner, Genome Res 2004 14 6 1188 1190 10.1101/gr.849004 15173120
    • (2004) Genome Res , vol.14 , Issue.6 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2    Chandonia, J.M.3    Brenner, S.E.4
  • 41
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • 10.1093/molbev/msm092. 17488738
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 42
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 10.1093/nar/22.22.4673. 7984417
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 10.1093/nar/22.22.4673 7984417
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3


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