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Volumn 32, Issue 4, 2015, Pages 970-977

Human long noncoding RNAs are substantially less folded than messenger RNAs

Author keywords

evolutionary rate; expression level; lncRNA; mRNA; RNA folding; translation

Indexed keywords

CYTOSINE DERIVATIVE; GUANINE DERIVATIVE; LONG UNTRANSLATED RNA; MESSENGER RNA;

EID: 84926650210     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu402     Document Type: Article
Times cited : (27)

References (50)
  • 1
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP.(2004).MicroRNAs: genomics, biogenesis, mechanism, and function.Cell 116:281-297
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 3
    • 30744432134 scopus 로고    scopus 로고
    • Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    • Chamary JV, Hurst LD.(2005).Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals.Genome Biol.6:R75
    • (2005) Genome Biol , vol.6 , pp. R75
    • Chamary, J.V.1    Hurst, L.D.2
  • 5
    • 84893427735 scopus 로고    scopus 로고
    • In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
    • Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM.(2014).In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.Nature 505:696-700
    • (2014) Nature , vol.505 , pp. 696-700
    • Ding, Y.1    Tang, Y.2    Kwok, C.K.3    Zhang, Y.4    Bevilacqua, P.C.5    Assmann, S.M.6
  • 6
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond DA, Wilke CO.(2008).Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.Cell 134:341-352
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 8
    • 54149095553 scopus 로고    scopus 로고
    • Biological principles of microRNAmediated regulation: Shared themes amid diversity
    • Flynt AS, Lai EC.(2008).Biological principles of microRNAmediated regulation: shared themes amid diversity.Nat Rev Genet.9:831-842
    • (2008) Nat Rev Genet , vol.9 , pp. 831-842
    • Flynt, A.S.1    Lai, E.C.2
  • 9
    • 84886252113 scopus 로고    scopus 로고
    • RNA in unexpected places: Long non-coding RNA functions in diverse cellular contexts
    • Geisler S, Coller J.(2013).RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts.Nat Rev Mol Cell Biol.14: 699-712
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 699-712
    • Geisler, S.1    Coller, J.2
  • 10
    • 77649198142 scopus 로고    scopus 로고
    • A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
    • Gu W, Zhou T, Wilke CO.(2010).A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes.PLoS Comput Biol.6:e1000664
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000664
    • Gu, W.1    Zhou, T.2    Wilke, C.O.3
  • 11
    • 84879969127 scopus 로고    scopus 로고
    • Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
    • Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES.(2013).Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.Cell 154:240-251
    • (2013) Cell , vol.154 , pp. 240-251
    • Guttman, M.1    Russell, P.2    Ingolia, N.T.3    Weissman, J.S.4    Lander, E.S.5
  • 12
    • 84878082656 scopus 로고    scopus 로고
    • Mutations within lncRNAs are effectively selected against in fruitfly but not in human
    • Haerty W, Ponting CP.(2013).Mutations within lncRNAs are effectively selected against in fruitfly but not in human.Genome Biol.14:R49
    • (2013) Genome Biol , vol.14 , pp. R49
    • Haerty, W.1    Ponting, C.P.2
  • 13
    • 84856397817 scopus 로고    scopus 로고
    • Analysis of energy-based algorithms for RNA secondary structure prediction
    • Hajiaghayi M, Condon A, Hoos HH.(2012).Analysis of energy-based algorithms for RNA secondary structure prediction.BMC Bioinformatics 13:22
    • (2012) BMC Bioinformatics , vol.13 , pp. 22
    • Hajiaghayi, M.1    Condon, A.2    Hoos, H.H.3
  • 14
    • 84899833919 scopus 로고    scopus 로고
    • Elements and machinery of noncoding RNAs: Toward their taxonomy
    • Hirose T, Mishima Y, Tomari Y.(2014).Elements and machinery of noncoding RNAs: toward their taxonomy.EMBO Rep.15:489-507
    • (2014) EMBO Rep , vol.15 , pp. 489-507
    • Hirose, T.1    Mishima, Y.2    Tomari, Y.3
  • 15
    • 0141519339 scopus 로고    scopus 로고
    • Widespread selection for local RNA secondary structure in coding regions of bacterial genes
    • Katz L, Burge CB.(2003).Widespread selection for local RNA secondary structure in coding regions of bacterial genes.Genome Res.13: 2042-2051
    • (2003) Genome Res , vol.13 , pp. 2042-2051
    • Katz, L.1    Burge, C.B.2
  • 16
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E.(2007).The role of site accessibility in microRNA target recognition.Nat Genet.39: 1278-1284
    • (2007) Nat Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 18
    • 26444450722 scopus 로고    scopus 로고
    • Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
    • Kondrashov FA.(2005).Prediction of pathogenic mutations in mitochondrially encoded human tRNAs.Hum Mol Genet.14: 2415-2419
    • (2005) Hum Mol Genet , vol.14 , pp. 2415-2419
    • Kondrashov, F.A.1
  • 19
  • 20
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla G, Murray AW, Tollervey D, Plotkin JB.(2009).Coding-sequence determinants of gene expression in Escherichia coli.Science 324: 255-258
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 23
    • 84871069553 scopus 로고    scopus 로고
    • Epigenetic regulation by long noncoding RNAs
    • Lee JT.(2012).Epigenetic regulation by long noncoding RNAs.Science 338: 1435-1439
    • (2012) Science , vol.338 , pp. 1435-1439
    • Lee, J.T.1
  • 25
    • 84858798657 scopus 로고    scopus 로고
    • Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
    • Managadze D, Rogozin IB, Chernikova D, Shabalina SA, Koonin EV.(2011).Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs.Genome Biol Evol.3: 1390-1404
    • (2011) Genome Biol Evol , vol.3 , pp. 1390-1404
    • Managadze, D.1    Rogozin, I.B.2    Chernikova, D.3    Shabalina, S.A.4    Koonin, E.V.5
  • 26
    • 33746320475 scopus 로고    scopus 로고
    • Revolutions in RNA secondary structure prediction
    • Mathews DH.(2006).Revolutions in RNA secondary structure prediction.J Mol Biol.359:526-532
    • (2006) J Mol Biol , vol.359 , pp. 526-532
    • Mathews, D.H.1
  • 27
    • 7444244924 scopus 로고    scopus 로고
    • Assigning pathogenicity to mitochondrial tRNA mutations: When "definitely maybe"is not good enough
    • McFarland R, Elson JL, Taylor RW, Howell N, Turnbull DM.(2004).Assigning pathogenicity to mitochondrial tRNA mutations: when "definitely maybe" is not good enough.Trends Genet.20: 591-596
    • (2004) Trends Genet , vol.20 , pp. 591-596
    • McFarland, R.1    Elson, J.L.2    Taylor, R.W.3    Howell, N.4    Turnbull, D.M.5
  • 29
    • 84883214592 scopus 로고    scopus 로고
    • Sizing up long noncoding RNAs: Do lncRNAs have secondary and tertiary structure?
    • Novikova IV, Hennelly SP, Sanbonmatsu KY.(2012).Sizing up long noncoding RNAs: do lncRNAs have secondary and tertiary structure?.Bioarchitecture 2:189-199
    • (2012) Bioarchitecture , vol.2 , pp. 189-199
    • Novikova, I.V.1    Hennelly, S.P.2    Sanbonmatsu, K.Y.3
  • 30
    • 84866449925 scopus 로고    scopus 로고
    • Prediction of variable translation rate effects on cotranslational protein folding
    • OBrien EP, Vendruscolo M, Dobson CM.(2012).Prediction of variable translation rate effects on cotranslational protein folding.Nat Commun.3:868
    • (2012) Nat Commun , vol.3 , pp. 868
    • O'Brien, E.P.1    Vendruscolo, M.2    Dobson, C.M.3
  • 31
    • 84874250754 scopus 로고    scopus 로고
    • Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly
    • Park C, Chen X, Yang JR, Zhang J.(2013).Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly.Proc Natl Acad Sci U S A.110:E678-E686
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. E678-E686
    • Park, C.1    Chen, X.2    Yang, J.R.3    Zhang, J.4
  • 32
    • 84901850307 scopus 로고    scopus 로고
    • Cell biology Lengthy RNAs earn respect as cellular players
    • Pennisi E.(2014).Cell biology.Lengthy RNAs earn respect as cellular players.Science 344:1072
    • (2014) Science , vol.344 , pp. 1072
    • Pennisi, E.1
  • 33
    • 34248162440 scopus 로고    scopus 로고
    • Functionality or transcriptional noise?.Evidence for selection within long noncoding RNAs
    • Ponjavic J, Ponting CP, Lunter G.(2007).Functionality or transcriptional noise?.Evidence for selection within long noncoding RNAs.Genome Res.17:556-565
    • (2007) Genome Res , vol.17 , pp. 556-565
    • Ponjavic, J.1    Ponting, C.P.2    Lunter, G.3
  • 34
    • 79959676389 scopus 로고    scopus 로고
    • The ribosome uses two active mechanisms to unwind messenger RNA during translation
    • Qu X, Wen JD, Lancaster L, Noller HF, Bustamante C, Tinoco I Jr.(2011).The ribosome uses two active mechanisms to unwind messenger RNA during translation.Nature 475:118-121
    • (2011) Nature , vol.475 , pp. 118-121
    • Qu, X.1    Wen, J.D.2    Lancaster, L.3    Noller, H.F.4    Bustamante, C.5    Tinoco, I.6
  • 35
    • 84893351549 scopus 로고    scopus 로고
    • Genomewide probing of RNA structure reveals active unfolding of mRNA structures in vivo
    • Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS.(2014).Genomewide probing of RNA structure reveals active unfolding of mRNA structures in vivo.Nature 505:701-705
    • (2014) Nature , vol.505 , pp. 701-705
    • Rouskin, S.1    Zubradt, M.2    Washietl, S.3    Kellis, M.4    Weissman, J.S.5
  • 36
    • 84964315393 scopus 로고    scopus 로고
    • Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs
    • Schuler A, Ghanbarian AT, Hurst LD.(2014).Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs.Mol Biol Evol.31: 3164-3183
    • (2014) Mol Biol Evol , vol.31 , pp. 3164-3183
    • Schuler, A.1    Ghanbarian, A.T.2    Hurst, L.D.3
  • 37
    • 84864116955 scopus 로고    scopus 로고
    • RNA structure prediction: An overview of methods
    • Seetin MG, Mathews DH.(2012).RNA structure prediction: an overview of methods.Methods Mol Biol.905:99-122
    • (2012) Methods Mol Biol , vol.905 , pp. 99-122
    • Seetin, M.G.1    Mathews, D.H.2
  • 40
    • 77649245858 scopus 로고    scopus 로고
    • Translation efficiency is determined by both codon bias and folding energy
    • Tuller T, Waldman YY, Kupiec M, Ruppin E.(2010).Translation efficiency is determined by both codon bias and folding energy.Proc Natl Acad Sci U S A.107:3645-3650
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 3645-3650
    • Tuller, T.1    Waldman, Y.Y.2    Kupiec, M.3    Ruppin, E.4
  • 41
    • 84879987789 scopus 로고    scopus 로고
    • LincRNAs: Genomics, evolution, and mechanisms
    • Ulitsky I, Bartel DP.(2013).lincRNAs: genomics, evolution, and mechanisms.Cell 154:26-46
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 46
    • 0346743541 scopus 로고    scopus 로고
    • Impact of disease-related mitochondrial mutations on tRNA structure and function
    • Wittenhagen LM, Kelley SO.(2003).Impact of disease-related mitochondrial mutations on tRNA structure and function.Trends Biochem Sci.28:605-611
    • (2003) Trends Biochem Sci , vol.28 , pp. 605-611
    • Wittenhagen, L.M.1    Kelley, S.O.2
  • 47
    • 84905375893 scopus 로고    scopus 로고
    • Codon-by-codon modulation of translational speed and accuracy via mRNA folding
    • Yang JR, Chen X, Zhang J.(2014).Codon-by-codon modulation of translational speed and accuracy via mRNA folding.PLoS Biol.12:e1001910
    • (2014) PLoS Biol , vol.12 , pp. e1001910
    • Yang, J.R.1    Chen, X.2    Zhang, J.3
  • 48
    • 84859473329 scopus 로고    scopus 로고
    • Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
    • Yang JR, Liao BY, Zhuang SM, Zhang J.(2012).Protein misinteraction avoidance causes highly expressed proteins to evolve slowly.Proc Natl Acad Sci U S A.109:E831-E840
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. E831-E840
    • Yang, J.R.1    Liao, B.Y.2    Zhuang, S.M.3    Zhang, J.4
  • 49
    • 0000616205 scopus 로고
    • RNA secondary structures and their prediction
    • Zuker M, Sankoff D.(1984).RNA secondary structures and their prediction.Bull Math Biol.46:591-621
    • (1984) Bull Math Biol , vol.46 , pp. 591-621
    • Zuker, M.1    Sankoff, D.2
  • 50
    • 84857770146 scopus 로고    scopus 로고
    • Strong association between mRNA folding strength and protein abundance in Scerevisiae
    • Zur H, Tuller T.(2012).Strong association between mRNA folding strength and protein abundance in Scerevisiae.EMBO Rep.13: 272-277
    • (2012) EMBO Rep , vol.13 , pp. 272-277
    • Zur, H.1    Tuller, T.2


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