Transat-A method for detecting the conserved helices of functional rna structures, including transient, pseudo-knotted and alternative structures

PLoS Computational Biology

Volumn 6, Issue 6, 2010, Pages 1-13

  Wiebe, Nicholas J P ^a   Meyer, Irmtraud M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; FORECASTING; RNA;

ALTERNATIVE STRUCTURE; FOLDING PATHWAY; FOLDINGS; FUNCTIONAL FEATURES; IN-VIVO; PREDICTION METHODS; RNA STRUCTURES; STRUCTURAL FEATURE; STRUCTURE PREDICTION; TRANSAT;

GENES;

RNA;

ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC CONSERVATION; HEMODYNAMICS; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; PREDICTION; PROTEIN FOLDING; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; METHODOLOGY; NUCLEIC ACID DATABASE; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; MODELS, MOLECULAR; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

EID: 77955475692     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000823     Document Type: Article

References (98)

1. Eddy SR (2002) Computational genomics of noncoding RNA genes. Cell 109: 137-40.
2. Mattick JS, Makunin IV (2006) Non-coding RNA. Hum Mol Genet 15 Spec No 1: R17-29.
3. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1559-63.
4. Boyle J, Robillard G, Kim S (1980) Sequential folding of transfer RNA. A nuclear magnetic resonance study of successively longer tRNA fragments with a common 59 end. Journal of Molecular Biology 139: 601-625.
5. Kramer F, Mills D (1981) Secondary structure formation during RNA-synthesis. Nucleic Acids Research 9: 5109-5124.
6. Nudler E, Mironov A (2004) The riboswitch control of bacterial metabolism. Trends Biochem Sci 29: 11-17.
7. Winkler W (2005) Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Current Opinion in Chemical Biology 9: 594-602.
8. Tucker B, Breaker R (2005) Riboswitches as versatile gene control elements. Current Opinion in Structural Biology 15: 342-348.
9. Repsilber D, Wiese S, Rachen M, Schroder A, Riesner D, et al. (1999) Formation of metastable RNA structures by sequential folding during transcription: Time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis. RNA 5: 574-584.
10. Ro-Choi T, Choi Y (2003) Structural elements of dynamic RNA strings. Molecules and Cells 16: 201-210.
11. Mathews D, Sabina J, Zuker M, Turner D (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.
12. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406-3415.
13. Hofacker I, Fontana W, Stadler P, Bonhoeffer S, Tacker M, et al. (1994) Fast Folding and Comparison of RNA Secondary Strutures. Monatshefte fü r Chemie (Chemical Monthly) 125: 167-188.
14. Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information. Nucleic Acids Research 9: 133-148.
15. Morgan S, Higgs P (1996) Evidence for kinetic effects in the folding of large RNA molecules. Journal of Chemical Physics 105: 7152-7157.
16. Meyer IM, Miklós I (2004) Co-transcriptional folding is encoded within RNA genes. BMC Molecular Biology 10: 5.
17. Hofacker I, Fekete M, Stadler P (2002) Secondary Structure Prediction for Aligned RNA Sequences. Journal of Molecular Biology 319: 1059-1066.
18. Witwer C (2003) Prediction of Conserved and Consensus RNA Structures. Ph.D. thesis, Universität Wien, Vienna, Austria.
19. Knudsen B, Hein J (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15: 446-454.
20. Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Research 31: 3423-3428.
21. Pedersen J, Forsberg R, Meyer I, Hein J (2004) An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol 21: 1913-1922.
22. Pedersen J, Meyer I, Forsberg R, Simmonds P, Hein J (2004) A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res 32: 4925-4936.
23. Ruan J, Stormo G, Zhang W (2004) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 20: 58-66.
24. Mathews DH, Turner DH (2002) Dynalign: An Algorithm for Finding the Secondary Structure Common to Two RNA Sequences. Journal of Molecular Biology 317: 191-203.
25. Mathews DH (2005) Predicting a Set of Minimal Free Energy RNA Secondary Structures Common to Two Sequences. Bioinformatics 21: 2246-2253.
26. Havgaard JH, Lyngsø RB, Stormo GD, Gorodkin J (2005) Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 21: 1815-1824.
27. Perriquet O, Touzet H, M D (2003) Finding the common structure shared by two homologous RNAs. Bioinformatics 19: 108-116.
28. Touzet H, Perriquet O (2004) CARNAC: folding families of related RNAs. Nucleic Acids Research 32: W142-145.
29. Ji Y, Xu X, Stormo G (2004) A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics 20: 1591-1602.
30. Holmes I (2005) Accelerated Probabilistic Inference of RNA Structure Evolution. BMC Bioinformatics 6: 73.
31. Dowell RD, Eddy SR (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 7: 400.
32. Meyer IM, Miklós I (2007) Simulfold: Simultaneously Inferring an RNA Structure Including Pseudo-Knots, a Multiple Sequence Alignment and an Evolutionary Tree Using a Bayesian Markov Chain Monte Carlo Framework. PLoS Computational Biology 3: e149.
33. Gardner PP, Giegerich R (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140.
34. Wuchty S, Fontana W, Hofacker I, Schuster P (1999) Complete suboptimal folding of rna and the stability of secondary structures. Biopolymers 49: 145-165.
35. Voss B, Giegerich R, Rehmsmeier M (2006) Complete probabilistic analysis of rna shapes. BMC Biol 4: 5.
36. Janssen S, Giegerich R (2010) Faster computation of exact RNA shape probabilities. Bioinformatics 26: 632-639.
37. Ding Y, Lawrence CE (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31: 7280-301.
38. Lewicki B, Margus T, Remme J, Nierhaus K (1993) Coupling of rRNA transcription and ribosomal assembly in vivo - formation of active ribosomalsubunits in Escherichia coli requires transcription of RNA genes by host RNA polymerase which cannot be replaced by T7 RNA polymerase. Journal of Molecular Biology 231: 581-593.
39. Chao MY, Kan M, Lin-Chao S (1995) RNAII transcribed by IPTG-induced T7 RNA polymerase is non-functional as a replication primer for ColE1-type plasmids in Escherichia coli. Nucleic Acids Research 23: 1691-1695.
40. Neugebauer K (2002) On the importance of being co-transcriptional. Journal of Cell Science 115: 3865-3871.
41. Morse D, Aruscavage P, Bass B (2002) RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proceedings of the National Academy of Science of the USA 99: 7906-7911.
42. Herschlag D (1995) RNA chaperones and the RNA folding problem. Journal of Biological Chemistry 270: 20871-20874.
43. Winkler W, Nahvi A, Roth A, Collins J, Breaker R (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
44. Lee R, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
45. Pyle A (2002) Metal ions in the structure and function of RNA. Journal of Biological Inorganic Chemistry 7: 679-690.
46. Heilmann-Miller SL, Woodson SA (2003) Effect of transcription on folding of the Tetrahymena ribozyme. RNA 9: 722-733.
47. Zhang L, Bao P, Leibowitz M, Zhang Y (2009) Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the selfsplicing Candida intron. RNA 15: 1986-1992.
48. Mironov A, Dyakonova L, Kister A (1985) A theoretical analysis of the kinetics of RNA secondary structure formation. Journal of Biomolecular Structure and Dynamics 2: 953-962.
49. Mironov A, Lebedev V (1993) A kinetic model of RNA folding. BioSystems 30: 49-56.
50. Danilova L, Pervouchine D, Favorov A, Mironov A (2006) RNAkinetics: a web server that models secondary structure kinetics of an elongating RNA. Journal of Bioinformatics and Computational Biology 4: 589-596.
51. Flamm C, Fontana W, Hofacker IL, Schuster P (2000) RNA folding at elementary step resolution. RNA 6: 325-38.
52. Isambert H, Siggia ED (2000) Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc Natl Acad Sci U S A 97: 6515-20.
53. Xayaphoummine A, Bucher T, Thalmann F, Isambert H (2003) Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc Natl Acad Sci U S A 100: 15310-5.
54. Xayaphoummine A, Bucher T, Isambert H (2005) Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res 33: W605-10.
55. Mironov A, Kister A (1986) RNA secondary structure formation during transcription. Journal of Biomolecular Structure and Dynamics 4: 1-9.
56. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A 101: 7287-92.
57. Wong TN, Sosnick TR, Pan T (2007) Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A 104: 17995-18000.
58. Flamm C, Hofacker I, Stadler P, Wolfinger M (2002) Barrier trees of degenerate landscapes. Zeitschrift Fur Physikalische Chemie-International Journal of Research In Physical Chemistry & Chemical Physics 216: 155-173.
59. Wolfinger M, Svrcek-Seiler W, Flamm C, Hofacker I, Stadler P (2004) Efficient computation of RNA folding dynamics. Journal of Physics A-Mathematical and General 37: 4731-4741.
60. Tang X, Kirkpatrick B, Thomas S, Song G, Amato N (2005) Using motion planning to study rna folding kinetics. Journal of Computational Biology 12: 862-881.
61. Tang X, Thomas SL, Tapia L, Amato NM (2007) Tools for simulating and analyzing rna folding kinetics. In: Speed TP, Huang H, eds. RECOMB. Springer, volume 4453 of Lecture Notes in Computer Science. pp 268-282.
62. Zhang W, Chen S (2003) Analyzing the biopolymer folding rates and pathways using kinetic cluster method. Journal of Chemical Physics 119: 8716-8729.
63. Zhang W, Chen SJ (2006) Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis. Biophys J 90: 765-77.
64. Cao S, Chen SJ (2007) Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. J Mol Biol 367: 909-24.
65. Heine C, Scheuermann G, Flamm C, Hofacker IL, Stadler PF (2006) Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph 12: 781-788.
66. Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, et al. (2008) Folding kinetics of large RNAs. J Mol Biol 379: 160-173.
67. Manuch J, Thachuk C, Stacho L, Condon A (2009) NP-completeness of the direct energy barrier problem without pseudoknots. Proc 15th International Meeting on DNA Computing and Molecular Programming.
68. Onoa B, Jr IT (2004) RNA folding and unfolding. Current Opinion in Structural Biology 14: 374-379.
69. Krishanthi S, Karunatilaka S, Rueda D (2009) Single-molecule fluorescence studies of RNA: A decade's progress. Chemical Physics Letters 476: 1-10.
70. Clausen-Schaumann H, Seitz M, Krautbauer R, Gaub H (2000) Force spectroscopy with single bio-molecules. Current Opinion in Chemical Biology 4: 524-530.
71. Hyeon C, Thirumalai D (2006) Forced-unfolding and force-quench refolding of RNA hairpins. Biophysical Journal 90: 3410-3427.
72. Alemán E, Lamichhane R, Rueda D (2008) Exploring RNA folding one molecule at a time. Current Opinion in Chemical Biology 12: 647-654.
73. Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD (1992) Identifying constraints on the higher-order structure of rna: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 20: 5785-95.
74. Yeang C, Darot J, Noller H, Haussler D (2007) Detecting the coevolution of biosequences - An example of RNA interaction prediction. Molecular Biology and Evolution 24: 2119-2131.
75. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
76. Holmes I (2004) A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 5: 166.
77. Notredame C, Higgins D, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302: 205-217.
78. Washietl S, Hofacker I (2004) Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. Journal of Molecular Biology 342: 19-30.
79. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31: 439-41.
80. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33: D121-4.
81. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37: D136-40.
82. Eddy SR, Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Res 22: 2079-88.
83. Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics 25: 1335-7.
84. Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, et al. (2008) Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res 36: D5-12.
85. Gardner PP (2008) Personal communication.
86. Andronescu M, Bereg V, Hoos H, Condon A (2008) RNA STRAND: The RNA Secondary Structure And Statistical Analysis Database. BMC Bioinformatics 9: 340.
87. Gerdes K, Larsen JE, Molin S (1985) Stable inheritance of plasmid R1 requires two different loci. J Bacteriol 161: 292-8.
88. Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND (1997) Antisense RNA-regulated programmed cell death. Annu Rev Genet 31: 1-31.
89. Gerdes K, Wagner EGH (2007) RNA antitoxins. Current Opinion In Microbiology 10: 117-124.
90. Gultyaev AP, Franch T, Gerdes K (1997) Programmed cell death by hok/sok of plasmid R1: coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs. J Mol Biol 273: 26-37.
91. Yanofsky C (2000) Transcription attenuation: once viewed as a novel regulatory strategy. J Bacteriol 182: 1-8.
92. Gollnick P, Babitzke P, Antson A, Yanofsky C (2005) Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annual Review of Genetics 39: 47-68.
93. Seliverstov AV, Putzer H, Gelfand MS, Lyubetsky VA (2005) Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria. BMC Microbiol 5: 54.
94. Voss B (2006) Structural analysis of aligned RNAs. Nucleic Acids Res 34: 5471-81.
95. Nagel JHA, Gultyaev AP, Oistämö KJ, Gerdes K, Pleij CWA (2002) A pH-jump approach for investigating secondary structure refolding kinetics in RNA. Nucleic Acids Res 30: e63.
96. Harlepp S, Marchal T, Robert J, Léger JF, Xayaphoummine A, et al. (2003) Probing complex RNA structures by mechanical force. Eur Phys J E Soft Matter 12: 605-15.
97. Gultyaev A, von Batenburg F, Pleij C (1995) The computer-simulation of RNA folding pathways using a genetic algorithm. Journal of Molecular Biology 250: 37-51.
98. Stadler P, Haslinger C RNA structures with pseudo-knots. Bulletin of Mathematical Biology 437-467.