1,240
Views
18
CrossRef citations to date
0
Altmetric
Research Paper

Using RNA inverse folding to identify IRES-like structural subdomains

, , &
Pages 1842-1852 | Received 22 Aug 2013, Accepted 30 Oct 2013, Published online: 04 Nov 2013

References

  • Martínez-Salas E, Pacheco A, Serrano P, Fernandez N. New insights into internal ribosome entry site elements relevant for viral gene expression. J Gen Virol 2008; 89:611 - 26; http://dx.doi.org/10.1099/vir.0.83426-0; PMID: 18272751
  • Filbin ME, Kieft JS. Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol 2009; 19:267 - 76; http://dx.doi.org/10.1016/j.sbi.2009.03.005; PMID: 19362464
  • Spriggs KA, Bushell M, Willis AE. Translational regulation of gene expression during conditions of cell stress. Mol Cell 2010; 40:228 - 37; http://dx.doi.org/10.1016/j.molcel.2010.09.028; PMID: 20965418
  • Liwak U, Faye MD, Holcik M. Translation control in apoptosis. Exp Oncol 2012; 34:218 - 30; PMID: 23070007
  • Komar AA, Hatzoglou M. Cellular IRES-mediated translation: the war of ITAFs in pathophysiological states. Cell Cycle 2011; 10:229 - 40; http://dx.doi.org/10.4161/cc.10.2.14472; PMID: 21220943
  • Martínez-Salas E. The impact of RNA structure on picornavirus IRES activity. Trends Microbiol 2008; 16:230 - 7; http://dx.doi.org/10.1016/j.tim.2008.01.013; PMID: 18420413
  • Fernández N, Fernandez-Miragall O, Ramajo J, García-Sacristán A, Bellora N, Eyras E, Briones C, Martínez-Salas E. Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation. Nucleic Acids Res 2011; 39:8572 - 85; http://dx.doi.org/10.1093/nar/gkr560; PMID: 21742761
  • Domingo E, Escarmis C, Martinez MA, Martinez-Salas E, Mateu MG. Foot-and-mouth disease virus populations are quasispecies. Curr Top Microbiol Immunol 1992; 176:33 - 47; http://dx.doi.org/10.1007/978-3-642-77011-1_3; PMID: 1318185
  • Pacheco A, Martinez-Salas E. Insights into the biology of IRES elements through riboproteomic approaches. J Biomed Biotechnol 2010; 2010:458927; http://dx.doi.org/10.1155/2010/458927; PMID: 20150968
  • Fernández N, García-Sacristán A, Ramajo J, Briones C, Martínez-Salas E. Structural analysis provides insights into the modular organization of picornavirus IRES. Virology 2011; 409:251 - 61; http://dx.doi.org/10.1016/j.virol.2010.10.013; PMID: 21056890
  • López de Quinto S, Martínez-Salas E. Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation. J Virol 1997; 71:4171 - 5; PMID: 9094703
  • Fernández-Miragall O, Martínez-Salas E. Structural organization of a viral IRES depends on the integrity of the GNRA motif. RNA 2003; 9:1333 - 44; http://dx.doi.org/10.1261/rna.5950603; PMID: 14561883
  • Robertson ME, Seamons RA, Belsham GJ. A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES. RNA 1999; 5:1167 - 79; http://dx.doi.org/10.1017/S1355838299990301; PMID: 10496218
  • Fernández-Miragall O, Ramos R, Ramajo J, Martínez-Salas E. Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA 2006; 12:223 - 34; http://dx.doi.org/10.1261/rna.2153206; PMID: 16373480
  • Jung S, Schlick T. Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site. Nucleic Acids Res 2013; 41:1483 - 95; http://dx.doi.org/10.1093/nar/gks1302; PMID: 23275533
  • Schnall-Levin M, Chindelevitch L, Berger B. In WW Cohen, A McCallum, SR Roweis (ed.) International Conference on Machine Learning 2008; volume 307. ACM International Conference Proceedings Series.
  • Bailor MH, Sun X, Al-Hashimi HM. Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science 2010; 327:202 - 6; http://dx.doi.org/10.1126/science.1181085; PMID: 20056889
  • Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res 2008; 36:Web Server issue W70-4; http://dx.doi.org/10.1093/nar/gkn188; PMID: 18424795
  • Busch A, Backofen R. INFO-RNA--a fast approach to inverse RNA folding. Bioinformatics 2006; 22:1823 - 31; http://dx.doi.org/10.1093/bioinformatics/btl194; PMID: 16709587
  • Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A. A new algorithm for RNA secondary structure design. J Mol Biol 2004; 336:607 - 24; http://dx.doi.org/10.1016/j.jmb.2003.12.041; PMID: 15095976
  • Taneda A. MODENA: a multi-objective RNA inverse folding. Adv Appl Bioinform Chem 2011; 4:1 - 12; PMID: 21918633
  • Zadeh JN, Wolfe BR, Pierce NA. Nucleic acid sequence design via efficient ensemble defect optimization. J Comput Chem 2011; 32:439 - 52; http://dx.doi.org/10.1002/jcc.21633; PMID: 20717905
  • Garcia-Martin JA, Clote P, Dotu I. RNAiFOLD: a constraint programming algorithm for rna inverse folding and molecular design. J Bioinform Comput Biol 2013; 11:1350001; http://dx.doi.org/10.1142/S0219720013500017; PMID: 23600819
  • Hisatake K, Ohta T, Takada R, Guermah M, Horikoshi M, Nakatani Y, Roeder RG. Evolutionary conservation of human TATA-binding-polypeptide-associated factors TAFII31 and TAFII80 and interactions of TAFII80 with other TAFs and with general transcription factors. Proc Natl Acad Sci U S A 1995; 92:8195 - 9; http://dx.doi.org/10.1073/pnas.92.18.8195; PMID: 7667268
  • Shao H, Revach M, Moshonov S, Tzuman Y, Gazit K, Albeck S, Unger T, Dikstein R. Core promoter binding by histone-like TAF complexes. Mol Cell Biol 2005; 25:206 - 19; http://dx.doi.org/10.1128/MCB.25.1.206-219.2005; PMID: 15601843
  • Scheer E, Delbac F, Tora L, Moras D, Romier C. TFIID TAF6-TAF9 complex formation involves the HEAT repeat-containing C-terminal domain of TAF6 and is modulated by TAF5 protein. J Biol Chem 2012; 287:27580 - 92; http://dx.doi.org/10.1074/jbc.M112.379206; PMID: 22696218
  • Wright KJ, Marr MT 2nd, Tjian R. TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter. Proc Natl Acad Sci U S A 2006; 103:12347 - 52; http://dx.doi.org/10.1073/pnas.0605499103; PMID: 16895980
  • Martínez-Salas E, Piñeiro D, Fernández N. Alternative Mechanisms to Initiate Translation in Eukaryotic mRNAs. Comp Funct Genomics 2012; 2012:391546; http://dx.doi.org/10.1155/2012/391546; PMID: 22536116
  • Herbreteau CH, Weill L, Décimo D, Prévôt D, Darlix JL, Sargueil B, Ohlmann T. HIV-2 genomic RNA contains a novel type of IRES located downstream of its initiation codon. Nat Struct Mol Biol 2005; 12:1001 - 7; http://dx.doi.org/10.1038/nsmb1011; PMID: 16244661
  • Henis-Korenblit S, Shani G, Sines T, Marash L, Shohat G, Kimchi A. The caspase-cleaved DAP5 protein supports internal ribosome entry site-mediated translation of death proteins. Proc Natl Acad Sci U S A 2002; 99:5400 - 5; http://dx.doi.org/10.1073/pnas.082102499; PMID: 11943866
  • Du X, Wang J, Zhu H, Rinaldo L, Lamar KM, Palmenberg AC, Hansel C, Gomez CM. Second cistron in CACNA1A gene encodes a transcription factor mediating cerebellar development and SCA6. Cell 2013; 154:118 - 33; http://dx.doi.org/10.1016/j.cell.2013.05.059; PMID: 23827678
  • Burkart C, Fan JB, Zhang DE. Two independent mechanisms promote expression of an N-terminal truncated USP18 isoform with higher DeISGylation activity in the nucleus. J Biol Chem 2012; 287:4883 - 93; http://dx.doi.org/10.1074/jbc.M111.255570; PMID: 22170061
  • Martínez-Salas E. Internal ribosome entry site biology and its use in expression vectors. Curr Opin Biotechnol 1999; 10:458 - 64; http://dx.doi.org/10.1016/S0958-1669(99)00010-5; PMID: 10508627
  • Fernández-Miragall O, López de Quinto S, Martínez-Salas E. Relevance of RNA structure for the activity of picornavirus IRES elements. Virus Res 2009; 139:172 - 82; http://dx.doi.org/10.1016/j.virusres.2008.07.009; PMID: 18692097
  • Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al, ENCODE Project Consortium, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children’s Hospital Oakland Research Institute. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799 - 816; http://dx.doi.org/10.1038/nature05874; PMID: 17571346
  • Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, et al. The reality of pervasive transcription. PLoS Biol 2011; 9:e1000625 - , discussion e1001102; http://dx.doi.org/10.1371/journal.pbio.1000625; PMID: 21765801
  • van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most “dark matter” transcripts are associated with known genes. PLoS Biol 2010; 8:e1000371; http://dx.doi.org/10.1371/journal.pbio.1000371; PMID: 20502517
  • Xue C, Li F, He T, Liu GP, Li Y, Zhang X. Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics 2005; 6:310; http://dx.doi.org/10.1186/1471-2105-6-310; PMID: 16381612
  • Ng KL, Mishra SK. De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics 2007; 23:1321 - 30; http://dx.doi.org/10.1093/bioinformatics/btm026; PMID: 17267435
  • Tjaden B. Prediction of small, noncoding RNAs in bacteria using heterogeneous data. J Math Biol 2008; 56:183 - 200; http://dx.doi.org/10.1007/s00285-007-0079-5; PMID: 17354017
  • Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100 - 8; http://dx.doi.org/10.1093/nar/gkm160; PMID: 17452365
  • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955 - 64; PMID: 9023104
  • Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005; 33:Web Server issue W686-9; http://dx.doi.org/10.1093/nar/gki366; PMID: 15980563
  • Freyhult E, Edvardsson S, Tamas I, Moulton V, Poole AM. Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update. BMC Res Notes 2008; 1:49; http://dx.doi.org/10.1186/1756-0500-1-49; PMID: 18710502
  • Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF. RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics 2010; 26:610 - 6; http://dx.doi.org/10.1093/bioinformatics/btp680; PMID: 20015949
  • Chang TH, Huang HD, Wu LC, Yeh CT, Liu BJ, Horng JT. Computational identification of riboswitches based on RNA conserved functional sequences and conformations. RNA 2009; 15:1426 - 30; http://dx.doi.org/10.1261/rna.1623809; PMID: 19460868
  • Singh P, Bandyopadhyay P, Bhattacharya S, Krishnamachari A, Sengupta S. Riboswitch detection using profile hidden Markov models. BMC Bioinformatics 2009; 10:325; http://dx.doi.org/10.1186/1471-2105-10-325; PMID: 19814811
  • Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D. ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol 2011; 8:11 - 3; http://dx.doi.org/10.4161/rna.8.1.13346; PMID: 21282983
  • Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009; 25:1335 - 7; http://dx.doi.org/10.1093/bioinformatics/btp157; PMID: 19307242
  • Zytnicki M, Gaspin C, Schiex T. Darn: a weighted constraint solver for RNA motif localization. Constraints 2008; 13:91 - 109; http://dx.doi.org/10.1007/s10601-007-9033-9
  • Gruber AR, Neuböck R, Hofacker IL, Washietl S. The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res 2007; 35:Web Server issue W335-8; http://dx.doi.org/10.1093/nar/gkm222; PMID: 17452347
  • Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res 2011; 21:1929 - 43; http://dx.doi.org/10.1101/gr.112516.110; PMID: 21994249
  • Hoeppner MP, Gardner PP, Poole AM. Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Comput Biol 2012; 8:e1002752; http://dx.doi.org/10.1371/journal.pcbi.1002752; PMID: 23133357
  • Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 2013; 41:Database issue D226 - 32; http://dx.doi.org/10.1093/nar/gks1005; PMID: 23125362
  • Rubin GM, Hong L, Brokstein P, Evans-Holm M, Frise E, Stapleton M, Harvey DA. A Drosophila complementary DNA resource. Science 2000; 287:2222 - 4; http://dx.doi.org/10.1126/science.287.5461.2222; PMID: 10731138
  • Martínez-Salas E, Sáiz JC, Dávila M, Belsham GJ, Domingo E. A single nucleotide substitution in the internal ribosome entry site of foot-and-mouth disease virus leads to enhanced cap-independent translation in vivo. J Virol 1993; 67:3748 - 55; PMID: 8389904
  • López de Quinto S, Sáiz M, de la Morena D, Sobrino F, Martínez-Salas E. IRES-driven translation is stimulated separately by the FMDV 3′-NCR and poly(A) sequences. Nucleic Acids Res 2002; 30:4398 - 405; http://dx.doi.org/10.1093/nar/gkf569; PMID: 12384586
  • Karabiber F, McGinnis JL, Favorov OV, Weeks KM. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA 2013; 19:63 - 73; http://dx.doi.org/10.1261/rna.036327.112; PMID: 23188808
  • Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P. Integrating chemical footprinting data into RNA secondary structure prediction. PLoS One 2012; 7:e45160; http://dx.doi.org/10.1371/journal.pone.0045160; PMID: 23091593
  • Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25:1974 - 5; http://dx.doi.org/10.1093/bioinformatics/btp250; PMID: 19398448
  • McGinnis JL, Duncan CD, Weeks KM. High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly. Methods Enzymol 2009; 468:67 - 89; http://dx.doi.org/10.1016/S0076-6879(09)68004-6; PMID: 20946765