Efficient algorithms for probing the RNA mutation landscape

PLoS Computational Biology

Volumn 4, Issue 8, 2008, Pages

  Waldispühl, Jérôme ^a,b   Devadas, Srinivas ^b   Berger, Bonnie ^a,b   Clote, Peter ^c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c BOSTON COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASES; FREE ENERGY; INTEGER PROGRAMMING; NUCLEOTIDES; STATISTICAL MECHANICS; VIRUSES;

CANONICAL ENSEMBLE; CELL-BE; CELL/B.E; CELL/BE; PARTITION FUNCTIONS; POINT WISE; RNA VIRUS; SECONDARY STRUCTURE PREDICTION; SECONDARY STRUCTURES; STATE-OF-THE-ART METHODS;

RNA;

VIRUS RNA; RNA;

3' UNTRANSLATED REGION; ALGORITHM; ARTICLE; CANONICAL ANALYSIS; EVOLUTION; GENE MUTATION; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTITION COEFFICIENT; RNA SEQUENCE; RNA STRUCTURE; RNA VIRUS; VIRUS REPLICATION; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONFORMATION; DNA RESPONSIVE ELEMENT; GENETICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; PHYSIOLOGY; REPLICON; THERMODYNAMICS;

HEPATITIS C VIRUS; RNA VIRUSES;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; HEPACIVIRUS; HIV; HUMANS; MUTAGENESIS; MUTATION; NUCLEIC ACID CONFORMATION; REPLICON; RESPONSE ELEMENTS; RNA; SOFTWARE; THERMODYNAMICS;

EID: 50949133711     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000124     Document Type: Article

References (53)

1. Coventry A, Kleitman DJ, Berger B (2004) Msari: multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci U S A 101: 12102-12107.
2. Rivas E, Eddy S (2001) Noncoding RNA gene detection using comparative sequence analysis. Bioinformatics 2: 8.
3. ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
4. Weinger JS, Parnell KM, Dorner S, Green R, Strobel SA (2004) Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat Struct Mol Biol 11: 1101-1106.
5. Omer A, Lowe T, Russell A, Ebhardt H, Eddy S, et al. (2000) Homologues of small nucleolar RNAs in Archaea. Science 288: 517-522.
6. Ambros V, Lee R, Lavanway A, Williams P, Jewell D (2003) MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol 13: 807-818.
7. Serganov A, Yuan Y, Pikovskaya O, Polonskaia A, Malinina L, et al. (2004) Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol 11: 1729-1741.
8. Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447: 497-500.
9. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR (2003) Rfam: an RNA family database. Nucleic Acids Res 31: 439-441.
10. 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-D124.
11. Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, et al. (2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2: e33. doi:10.1371/journal.pcbi.0020033.
12. Meyer IM, Miklos I (2007) Simulfold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol 3: e149. doi:10.1371/journal.pcbi. 0030149.
13. Xia T, SantaLucia JJ, Burkard ME, Kierzek R, Schroeder SJ, et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
14. Zuker M, Stiegler P (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9: 133-148.
15. Hofacker I, Fontana W, Stadler P, Bonhoeffer L, Tacker M, et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125: 167-188.
16. Dowell RD, Eddy SR (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 7: 400.
17. Harmanci AO, Sharma G, Mathews DH (2007) Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics 8: 130.
18. Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31: 3423-3428.
19. Mathews DH, Turner DH (2002) Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 317: 191-203.
20. McCaskill JS (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
21. Ding Y, Lawrence CE (1999) A Bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem 23: 387-400.
22. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
23. Hofacker I (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
24. Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32: W135-W141.
25. Barash D (2003) Deleterious mutation prediction in the secondary structure of RNAs. Nucleic Acids Res 31: 6578-6584.
26. Grüner W, Giegerich R, Strohmann D, Reidys C, Weber J, et al. (1996) Analysis of RNA sequence structure maps by exhaustive enumeration. Monatsh Chem 127: 355-374.
27. Reidys C, Stadler P, Schuster P (1997) Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull Math Biol 59: 339-397.
28. Schuster P, Fontana W, Stadler PF, Hofacker IL (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond B Biol Sci 255: 279-284.
29. Cowperthwaite MC, Meyers LA (2007) How mutational networks shape evolution: lessons from RNA models. Annu Rev Ecol Evol Syst 38: 203-230.
30. Gardner PP, Giegerich R (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140.
31. Mathews D, Sabina J, Zuker M, Turner H (1999) Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J Mol Biol 288: 911-940.
32. Waldispuhl J, Behzadi B, Steyaert JM (2002) An approximate matching algorithm for finding (sub-)optimal sequences in S-attributed grammars. Bioinformatics 18: S250-S259.
33. Clote P, Waldispuhl J, Behzadi B, Steyaert JM (2005) Energy landscape of k-point mutants of an RNA molecule. Bioinformatics 21: 4140-4147.
34. Nussinov R, Jacobson AB (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A 77: 6309-6313.
35. Shu W, Bo X, Liu R, Zhao D, Zheng Z, et al. (2006) RDMAS: a web server for RNA deleterious mutation analysis. BMC Bioinformatics 7: 404.
36. Baker B, Muckenthaler M, Vives E, Blanchard A, Braddock M, et al. (1994) Identification of a novel HIV-1 TAR RNA bulge binding protein. Nucleic Acids Res 22: 3365-3372.
37. Kulinski T, Olejniczak M, Huthoff H, Bielecki L, Pachulska-Wieczorek K, et al. (2003) The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a crossloop base pair. J Biol Chem 278: 38892-38901.
38. Yang M (2005) Discoveries of Tat-TAR interaction inhibitors for HIV-1. Curr Drug Targets Infect Disord 5: 433-444.
39. You S, Stump DD, Branch AD, Rice CM (2004) A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J Virol 78: 1352-1366.
40. Ponty Y (2007) Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method. J Math Biol 56: 107-127.
41. Waldispuhl J, Clote P (2007) Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. J Comput Biol 14: 190-215.
42. Hofacker IL, Stadler PF (2006) Modeling RNA folding. In: Deisboeck TS, Kresh JY, editors. Complex Systems Science in Biomedicine, New York: Spinger. pp. 227-245.
43. Ding Y, Chan CY, Lawrence CE (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11: 1157-1166.
44. Yanagi M, St Claire M, Shapiro M, Emerson SU, Purcell RH, et al. (1998) Transcripts of a chimeric cDNA clone of hepatitis C virus genotype 1b are infectious in vivo. Virology 244: 161-172.
45. Dimitrov RA, Zuker M (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J 87: 215-226.
46. Brown S, Wang L (2006) Prediction of RNA-binding residues in protein sequences using support vector machines. Conf Proc IEEE Eng Med Biol Soc 1:5830-5833. doi:10.1109/ IEMBS.2006.260025.
47. Thurner C, Witwer C, Hofacker IL, Stadler PF (2004) Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol 85: 1113-1124.
48. Cuceanu NM, Tuplin A, Simmonds P (2001) Evolutionarily conserved RNA secondary structures in coding and non-coding sequences at the 3′ end of the hepatitis G virus/GB-virus C genome. J Gen Virol 82: 713-722.
49. Bernhart SH, Hofacker IL, Stadler PF (2006) Local RNA base pairing probabilities in large sequences. Bioinformatics 22: 614-615.
50. Fontana W, Schuster P (1987) A computer model of evolutionary optimization. Biophys Chem 26: 123-147.
51. Schuster P (1993) RNA based evolutionary optimization. Orig Life Evol Biosph 23: 373-391.
52. Cowperthwaite MC, Bull JJ, Meyers LA (2005) Distributions of beneficial fitness effects in rna. Genetics 170: 1449-1457.
53. Miklos I, Meyer IM, Nagy B (2005) Moments of the Boltzmann distribution for RNA secondary structures. Bull Math Biol 67: 1031-1047.