Annotating RNA motifs in sequences and alignments

Nucleic Acids Research

Volumn 43, Issue 2, 2015, Pages 691-698

  Gardner, Paul P ^a   Eldai, Hisham ^a  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CHEMISTRY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; NUCLEOTIDE MOTIF; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL;

DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE ANNOTATION; NUCLEOTIDE MOTIFS; RNA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 84941062157     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1327     Document Type: Article

References (80)

1. Brownlee, G.G. (1971) Sequence of 6S RNA of E. coli. Nat. New Biol., 229, 147-149.
2. Barrick, J.E., Sudarsan, N., Weinberg, Z., Ruzzo, W.L., Breaker, R.R. (2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA, 11, 774-784.
3. Wassarman, K.M., Storz, G. (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell, 101, 613-623.
4. Lerner, M.R., Boyle, J.A., Hardin, J.A., Steitz, J.A. (1981) Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus. Science, 211, 400-402.
5. Christov, C.P., Gardiner, T.J., Sz üts, D., Krude, T. (2006) Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol. Cell. Biol., 26, 6993-7004.
6. Wang, Z., Gerstein, M., Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
7. Perkins, T.T., Kingsley, R.A., Fookes, M.C., Gardner, P.P., James, K.D., Yu, L., Assefa, S.A., He, M., Croucher, N.J., Pickard, D.J. et al. (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet., 5, e1000569.
8. Lindgreen, S., Umu, S.U., Lai, A.S., Eldai, H., Liu, W., McGimpsey, S., Wheeler, N.E., Biggs, P.J., Thomson, N.R., Barquist, L. et al. (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput. Biol., 10, e1003907.
9. Westhof, E., Romby, P. (2010) The RNA structurome: high-throughput probing. Nat. Methods, 7, 965-967.
10. Barquist, L., Langridge, G.C., Turner, D.J., Phan, M.D., Turner, A.K., Bateman, A., Parkhill, J., Wain, J., Gardner, P.P. (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res.41, 4549-4564.
11. Barquist, L., Boinett, C.J., Cain, A.K. (2013) Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol., 10, 1161-1169.
12. Gardner, P.P., Daub, J., Tate, J., Moore, B.L., Osuch, I.H., Griffiths-Jones, S., Finn, R.D., Nawrocki, E.P., Kolbe, D.L., Eddy, S.R. et al. (2011) Rfam: Wikipedia, clans and the decimal release. Nucleic Acids Res., 39, D141-D145.
13. Burge, S.W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E.P., Eddy, S.R., Gardner, P.P., Bateman, A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41, D226-D232.
14. Nawrocki, E.P., Burge, S.W., Bateman, A., Daub, J., Eberhardt, R.Y., Eddy, S.R., Floden, E.W., Gardner, P.P., Jones, T.A., Tate, J. et al. (2014) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res., doi:10.1093/nar/gku1063.
15. Eddy, S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
16. Hoeppner, M.P., Gardner, P.P., Poole, A.M. (2012) Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput. Biol., 8, e1002752.
17. Jaeger, L., Michel, F., Westhof, E. (1994) Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol., 236, 1271-1276.
18. Jucker, F.M., Heus, H.A., Yip, P.F., Moors, E.H., Pardi, A. (1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol., 264, 968-980.
19. Abramovitz, D.L., Pyle, A.M. (1997) Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. J. Mol. Biol., 266, 493-506.
20. Lucchetti-Miganeh, C., Burrowes, E., Baysse, C., Ermel, G. (2008) The post-transcriptional regulator CsrA plays a central role in the adaptation of bacterial pathogens to different stages of infection in animal hosts. Microbiology, 154, 16-29.
21. Valverde, C., Lindell, M., Wagner, E.G., Haas, D. (2004) A repeated GGA motif is critical for the activity and stability of the riboregulator RsmY of Pseudomonas fluorescens. J. Biol. Chem., 279, 25066-25074.
22. Toledo-Arana, A., Repoila, F., Cossart, P. (2007) Small noncoding RNAs controlling pathogenesis. Curr. Opin. Microbiol., 10, 182-188.
23. Batey, R.T., Rambo, R.P., Lucast, L., Rha, B., Doudna, J.A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science, 287, 1232-1239.
24. López de Silanes, I., Zhan, M., Lal, A., Yang, X., Gorospe, M. (2004) Identification of a target RNA motif for RNA-binding protein HuR. Proc. Natl. Acad. Sci. U.S.A., 101, 2987-2992.
25. Yao, Z., Weinberg, Z., Ruzzo, W.L. (2006) CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics, 22, 445-452.
26. Gorodkin, J., Stricklin, S.L., Stormo, G.D. (2001) Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res., 29, 2135-2144.
27. Höchsmann, M., T oller, T., Giegerich, R., Kurtz, S. (2003) Local similarity in RNA secondary structures. Proc. IEEE Comput. Soc. Bioinform. Conf., 2, 159-168.
28. Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A., Leontis, N.B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol., 56, 215-252.
29. Macke, T.J., Ecker, D.J., Gutell, R.R., Gautheret, D., Case, D.A., Sampath, R. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res., 29, 4724-4735.
30. Naville, M., Ghuillot-Gaudeffroy, A., Marchais, A., Gautheret, D. (2011) ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol., 8, 11-13.
31. Gardner, P.P., Barquist, L., Bateman, A., Nawrocki, E.P., Weinberg, Z. (2011) RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Res., 14, 5845-5852.
32. Cruz, J.A.,Westhof, E. (2011) Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat. Methods, 8, 513-521.
33. Haussler, D., Krogh, A., Mian, I., Sjolander, K. (1993) Protein modeling using hidden Markov models: analysis of globins. In: Proceedings of the Twenty-Sixth Hawaii International Conference on System Sciences, 1993, Vol. i, pp. 792-802.
34. Krogh, A. (1994) Hidden Markov models for labelled sequences. Proceedings of the 12th IAPR International Conference on Pattern Recognition, Vol. 2, pp. 140-144.
35. Durbin, R., Eddy, S., Krogh, A., Mitchison, G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge.
36. Eddy, S.R., Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
37. Sakakibara, Y., Brown, M., Hughey, R., Mian, I.S., Sj ölander, K., Underwood, R.C., Haussler, D. (1994) Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res., 22, 5112-5120.
38. Gardner, P.P., Fasold, M., Burge, S.W., Ninova, M., Hertel, J., Kehr, S., Steeves, T.E., Griffiths-Jones, S., Stadler, P.F. (2014) Conservation and losses non-coding RNA associated loci in avian genomes. Genomics, arXiv:1406.7140.
39. Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., Eddy, S.R. (2003) Rfam: an RNA family database. Nucleic Acids Res., 31, 439-441.
40. Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., Bateman, A. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
41. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
42. Doshi, K.J., Cannone, J.J., Cobaugh, C.W., Gutell, R.R. (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics, 5, 105-105.
43. Weinberg, Z., Ruzzo, W.L. (2006) Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics, 22, 35-39.
44. Nawrocki, E.P., Kolbe, D.L., Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
45. Freyhult, E.K., Bollback, J.P., Gardner, P.P. (2007) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res., 17, 117-125.
46. Kolbe, D.L., Eddy, S.R. (2011) Fast filtering for RNA homology search. Bioinformatics, 27, 3102-3109.
47. Nawrocki, E.P., Eddy, S.R. (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol., 3, e56.
48. Weinberg, Z., Ruzzo, W.L. (2004) Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics, 20(Suppl. 1), i334-i341.
49. Schroeder, K.T., McPhee, S.A., Ouellet, J., Lilley, D.M. (2010) A structural database for k-turn motifs in RNA. RNA, 16, 1463-1468.
50. Klosterman, P.S., Hendrix, D.K., Tamura, M., Holbrook, S.R., Brenner, S.E. (2004) Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Res., 32, 2342-2352.
51. Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R., Brenner, S.E., Holbrook, S.R. (2004) SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res., 32, D182-D184.
52. Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Müller, K.M. et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics, 3, 2.
53. Zhong, C., Zhang, S. (2012) Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment. Nucleic Acids Res., 40, 1307-1317.
54. Petrov, A.I., Zirbel, C.L., Leontis, N.B. (2011) WebFR3D-a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res., 39, W50-W55.
55. Zirbel, C.L., Sponer, J.E., Sponer, J., Stombaugh, J., Leontis, N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
56. Grabow, W.W., Zhuang, Z., Swank, Z.N., Shea, J.E., Jaeger, L. (2012) The right angle (RA) motif: a prevalent ribosomal RNA structural pattern found in group I introns. J. Mol. Biol., 424, 54-67.
57. Rosenblad, M.A., Larsen, N., Samuelsson, T., Zwieb, C. (2009) Kinship in the SRP RNA family. RNA Biol., 6, 508-516.
58. Popenda, M., Blazewicz, M., Szachniuk, M., Adamiak, R.W. (2008) RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res., 36, D386-D391.
59. Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E.K., Blazewicz, J., Adamiak, R.W. (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics, 11, 231.
60. Bluhm, W.F., Beran, B., Bi, C., Dimitropoulos, D., Prlic, A., Quinn, G.B., Rose, P.W., Shah, C., Young, J., Yukich, B. et al. (2011) Quality assurance for the query and distribution systems of the RCSB Protein Data Bank. Database, 2011, 003.
61. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
62. Consortium, PDB (2014 ) PDB derived data, PDB FTP site. http://ftp.wwpdb.org/pub/pdb/derived data/pdb seqres.txt.gz.
63. Leinonen, R., Akhtar, R., Birney, E., Bonfield, J., Bower, L., Corbett, M., Cheng, Y., Demiralp, F., Faruque, N., Goodgame, N. et al. (2010) Improvements to services at the European Nucleotide Archive. Nucleic Acids Res., 38, D39-D45.
64. Workman, C., Krogh, A. (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res., 27, 4816-4822.
65. Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
66. Weinberg, Z., Breaker, R.R. (2011) R2R-software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics, 12, 3.
67. Weinberg, Z., Wang, J.X., Bogue, J., Yang, J., Corbino, K., Moy, R.H., Breaker, R.R. (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes. Genome Biol., 11, R31.
68. Leonardi, J., Box, J.A., Bunch, J.T., Baumann, P. (2008) TER1, the RNA subunit of fission yeast telomerase. Nat. Struct. Mol. Biol., 15, 26-33.
69. Webb, C.J., Zakian, V.A. (2008) Identification and characterization of the Schizosaccharomyces pombe TER1 telomerase RNA. Nat. Struct. Mol. Biol., 15, 34-42.
70. Gardner, P.P., Bateman, A., Poole, A.M. (2010) SnoPatrol: how many snoRNA genes are there? J. Biol., 9, 4.
71. Bateman, A., Agrawal, S., Birney, E., Bruford, E.A., Bujnicki, J.M., Cochrane, G., Cole, J.R., Dinger, M.E., Enright, A.J., Gardner, P.P. et al. (2011) RNAcentral: a vision for an international database of RNA sequences. RNA, 17, 1941-1946.
72. Widmann, J., Stombaugh, J., McDonald, D., Chocholousova, J., Gardner, P., Iyer, M.K., Liu, Z., Lozupone, C.A., Quinn, J., Smit, S. et al. (2012) RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA, 18, 1319-1327.
73. Duss, O., Michel, E., Yulikov, M., Schubert, M., Jeschke, G., Allain, F.H. (2014) Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature, 509, 588-592.
74. Schubert, M., Lapouge, K., Duss, O., Oberstrass, F.C., Jelesarov, I., Haas, D., Allain, F.H. (2007) Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat. Struct. Mol. Biol., 14, 807-813.
75. Barquist, L., Burge, S.W., Gardner, P.P. (2012) Building non-coding RNA families. Biomolecules, arXiv:1206.4087.
76. Gardner, P.P., Giegerich, R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5, 140.
77. Simons, K.T., Kooperberg, C., Huang, E., Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
78. Granneman, S., Kudla, G., Petfalski, E., Tollervey, D. (2009) Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proc. Natl. Acad. Sci. U.S.A., 106, 9613-9618.
79. Jungkamp, A.C., Stoeckius, M., Mecenas, D., Grn, D., Mastrobuoni, G., Kempa, S., Rajewsky, N. (2011) In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol. Cell, 44, 828-840.
80. Ray, D., Kazan, H., Cook, K.B., Weirauch, M.T., Najafabadi, H.S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A. et al. (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature, 499, 172-177.