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RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

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Abstract

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation (1H–15N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy (1H–1H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a majority of the NMR resonances, even when the initial predictions are only modestly accurate. RNA-PAIRS is available as a public web-server at http://pine.nmrfam.wisc.edu/RNA/.

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References

  • Ampt KAM, van der Werf RM, Nelissen FHT et al (2009) The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding. Biochemistry 48:10499–10508. doi:10.1021/bi9011385

    Article  Google Scholar 

  • Andronescu M, Aguirre-Hernández R, Condon A, Hoos HH (2003) RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res 31:3416–3422

    Article  Google Scholar 

  • Bahrami A, Assadi AH, Markley JL, Eghbalnia HR (2009) Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol 5:e1000307. doi:10.1371/journal.pcbi.1000307

    Article  Google Scholar 

  • Berjanskii M, Tang P, Liang J et al (2009) GeNMR: a web server for rapid NMR-based protein structure determination. Nucleic Acids Res 37:W670–W677. doi:10.1093/nar/gkp280

    Article  Google Scholar 

  • Clote P (2005) RNALOSS: a web server for RNA locally optimal secondary structures. Nucleic Acids Res 33:W600–W604. doi:10.1093/nar/gki382

    Article  Google Scholar 

  • Cornish PV, Hennig M, Giedroc DP (2005) A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc Natl Acad Sci USA 102:12694–12699. doi:10.1073/pnas.0506166102

    Article  ADS  Google Scholar 

  • Cromsigt JA, Hilbers CW, Wijmenga SS (2001) Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation. J Biomol NMR 21:11–29

    Article  Google Scholar 

  • D’Souza V, Dey A, Habib D, Summers MF (2004) NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J Mol Biol 337:427–442. doi:10.1016/j.jmb.2004.01.037

    Article  Google Scholar 

  • Davis JH, Tonelli M, Scott LG et al (2005) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J Mol Biol 351:371–382. doi:10.1016/j.jmb.2005.05.069

    Article  Google Scholar 

  • Desjardins G, Bonneau E, Girard N et al (2011) NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. Nucleic Acids Res 39:4427–4437. doi:10.1093/nar/gkq1244

    Article  Google Scholar 

  • Dimitrov RA, Zuker M (2004) Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J 87:215–226. doi:10.1529/biophysj.103.020743

    Article  Google Scholar 

  • Ding Y, Lawrence C (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31:7280–7301

    Article  Google Scholar 

  • Dirks RM, Lin M, Winfree E, Pierce NA (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res 32:1392–1403. doi:10.1093/nar/gkh291

    Article  Google Scholar 

  • Doshi KJ, Cannone JJ, Cobaugh CW, Gutell RR (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinform 5:105. doi:10.1186/1471-2105-5-105

    Article  Google Scholar 

  • Eghbalnia HR, Bahrami A, Wang L et al (2005a) Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO). J Biomol NMR 32:219–233. doi:10.1007/s10858-005-7944-6

    Article  Google Scholar 

  • Eghbalnia HR, Wang L, Bahrami A et al (2005b) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR 32:71–81. doi:10.1007/s10858-005-5705-1

    Article  Google Scholar 

  • Fourmy D, Yoshizawa S, Puglisi JD (1998) Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J Mol Biol 277:333–345. doi:10.1006/jmbi.1997.1551

    Article  Google Scholar 

  • Fox BG, Goulding C, Malkowski MG et al (2008) Structural genomics: from genes to structures with valuable materials and many questions in between. Nature Methods 5:129–132. doi:10.1038/nmeth0208-129

    Article  Google Scholar 

  • Fürtig B, Richter C, Wöhnert J, Schwalbe H (2003) NMR spectroscopy of RNA. Chembiochem 4:936–962. doi:10.1002/cbic.200300700

    Article  Google Scholar 

  • Georgii H-O (1988) Gibbs measures and phase transitions. W. de Gruyter, Berlin

    Book  MATH  Google Scholar 

  • Giedroc DP, Cornish PV (2009) Frameshifting RNA pseudoknots: structure and mechanism. Virus Res 139:193–208. doi:10.1016/j.virusres.2008.06.008

    Article  Google Scholar 

  • Gruber AR, Lorenz R, Bernhart SH et al (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70–W74. doi:10.1093/nar/gkn188

    Article  Google Scholar 

  • Güntert P (2009) Automated structure determination from NMR spectra. Eur Biophys J EBJ 38:129–143. doi:10.1007/s00249-008-0367-z

    Article  Google Scholar 

  • Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12:301–310

    Article  Google Scholar 

  • Hart JM, Kennedy SD, Mathews DH, Turner DH (2008) NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc 130:10233–10239. doi:10.1021/ja8026696

    Article  Google Scholar 

  • Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431

    Article  Google Scholar 

  • Hoogstraten CG, Legault P, Pardi A (1998) NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis. J Mol Biol 284:337–350. doi:10.1006/jmbi.1998.2182

    Article  Google Scholar 

  • Huang C, Darwiche A (1996) Inference in belief networks: a procedural guide. Int J Approx Reason 15:225–263

    Article  MathSciNet  MATH  Google Scholar 

  • Huppler A, Nikstad LJ, Allmann AM et al (2002) Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure. Nat Struct Biol 9:431–435. doi:10.1038/nsb800

    Article  Google Scholar 

  • Ihle Y, Ohlenschläger O, Häfner S et al (2005) A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA. Nucleic Acids Res 33:2003–2011. doi:10.1093/nar/gki501

    Article  Google Scholar 

  • Juan V, Wilson C (1999) RNA secondary structure prediction based on free energy and phylogenetic analysis. J Mol Biol 289:935–947. doi:10.1006/jmbi.1999.2801

    Article  Google Scholar 

  • Kang M, Peterson R, Feigon J (2009) Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell 33:784–790. doi:10.1016/j.molcel.2009.02.019

    Article  Google Scholar 

  • Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31:3423–3428

    Article  Google Scholar 

  • Kruschel D, Sigel RKO (2009) NMR solution structure of the d3′-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5(gamma). PDB doi:10.2210/pdb2k63/pdb

  • Kuhn HW (1955) The Hungarian method for the assignment problem. Naval Res Logist Q 2:83–97. doi:10.1002/nav.3800020109

    Article  Google Scholar 

  • Le SY, Chen JH, Maizel JVJ (1990) Efficient searches for unusual folding regions in RNA sequences. In: Sarma RH, Sarma MH (eds) Structure and methods: human genome initiative and DNA recombination. Adenine Press, Schenectady, pp 127–136

    Google Scholar 

  • Lukavsky PJ, Kim I, Otto GA, Puglisi JD (2003) Structure of HCV IRES domain II determined by NMR. Nat Struct Biol 10:1033–1038. doi:10.1038/nsb1004

    Article  Google Scholar 

  • MacQueen J (1967) Some methods for classification and analysis of multivariate observations. In: Le Cam LM, Neyman J (eds) Proceedings of the fifth Berkeley Symposium on Mathematical Statistics and Probability. University of California Press, pp 281–297

  • Marcheschi RJ, Staple DW, Butcher SE (2007) Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop. J Mol Biol 373:652–663. doi:10.1016/j.jmb.2007.08.033

    Article  Google Scholar 

  • Mathews DH (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA (New York, NY) 10:1178–1190. doi:10.1261/rna.7650904

    Article  Google Scholar 

  • Mathews DH, Turner DH (2006) Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol 16:270–278. doi:10.1016/j.sbi.2006.05.010

    Article  Google Scholar 

  • Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940. doi:10.1006/jmbi.1999.2700

    Article  Google Scholar 

  • Mathews DH, Disney MD, Childs JL et al (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101:7287–7292. doi:10.1073/pnas.0401799101

    Article  ADS  Google Scholar 

  • Matlab (2010) R2010a : the MathWorks Inc. Natick, MA

  • Miyazaki Y, Irobalieva RN, Tolbert B et al (2010) Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. J Mol Biol 404:751–772. doi:10.1016/j.jmb.2010.09.009

    Article  Google Scholar 

  • Morosyuk SV, Cunningham PR, SantaLucia J (2001) Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure. J Mol Biol 307:197–211. doi:10.1006/jmbi.2000.4431

    Article  Google Scholar 

  • Nagaswamy U, Larios-Sanz M, Hury J et al (2002) NCIR: a database of non-canonical interactions in known RNA structures. Nucleic Acids Res 30:395–397

    Article  Google Scholar 

  • Nozinovic S, Fürtig B, Jonker HRA et al (2010) High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Res 38:683–694. doi:10.1093/nar/gkp956

    Article  Google Scholar 

  • Palla G, Derényi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435:814–818. doi:10.1038/nature03607

    Article  ADS  Google Scholar 

  • Reiter NJ, Maher LJ, Butcher SE (2008) DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer. Nucleic Acids Res 36:1227–1236. doi:10.1093/nar/gkm1141

    Article  Google Scholar 

  • Rivas E, Eddy SR (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol 285:2053–2068. doi:10.1006/jmbi.1998.2436

    Article  Google Scholar 

  • Sashital DG, Cornilescu G, McManus CJ et al (2004) U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction. Nat Struct Mol Biol 11:1237–1242. doi:10.1038/nsmb863

    Article  Google Scholar 

  • Sashital DG, Venditti V, Angers CG et al (2007) Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. RNA (New York, NY) 13:328–338. doi:10.1261/rna.418407

    Article  Google Scholar 

  • Sato K, Hamada M, Asai K, Mituyama T (2009) CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res 37:W277–W280. doi:10.1093/nar/gkp367

    Article  Google Scholar 

  • Shen Y, Bax A (2010) SPARTA + : a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48:13–22. doi:10.1007/s10858-010-9433-9

    Article  Google Scholar 

  • Shen Y, Vernon R, Baker D, Bax A (2009) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43:63–78. doi:10.1007/s10858-008-9288-5

    Article  Google Scholar 

  • Smyth P (1997) Belief networks, hidden Markov models, and Markov random fields: a unifying view. Pattern Recogn Lett 18:1261–1268. doi:10.1016/S0167-8655(97)01050-7

    Article  ADS  Google Scholar 

  • Staple DW, Butcher SE (2003) Solution structure of the HIV-1 frameshift inducing stem-loop RNA. Nucleic Acids Res 31:4326–4331

    Article  Google Scholar 

  • Stich M, Lázaro E, Manrubia SC (2010) Phenotypic effect of mutations in evolving populations of RNA molecules. BMC Evol Biol 10:46. doi:10.1186/1471-2148-10-46

    Article  Google Scholar 

  • Stratmann D, Guittet E, van Heijenoort C (2010) Robust structure-based resonance assignment for functional protein studies by NMR. J Biomol NMR 46:157–173. doi:10.1007/s10858-009-9390-3

    Article  Google Scholar 

  • Tatikonda S, Jordan MI (2002) Loopy belief propagation and Gibbs measures. In Darwiche A, Friedman N (eds) UAI. Morgan Kaufmann, pp 493–500

  • Tavares TJ, Beribisky AV, Johnson PE (2009) Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin. RNA (New York, NY) 15:911–922. doi:10.1261/rna.1514909

    Article  Google Scholar 

  • Theimer CA, Finger LD, Trantirek L, Feigon J (2003) Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA. Proc Natl Acad Sci USA 100:449–454. doi:10.1073/pnas.242720799

    Article  ADS  Google Scholar 

  • Theimer CA, Blois CA, Feigon J (2005) Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Molecular cell 17:671–682. doi:10.1016/j.molcel.2005.01.017

    Article  Google Scholar 

  • Theimer CA, Jády BE, Chim N et al (2007) Structural and functional characterization of human telomerase RNA processing and cajal body localization signals. Mol Cell 27:869–881. doi:10.1016/j.molcel.2007.07.017

    Article  Google Scholar 

  • Ulrich EL, Akutsu H, Doreleijers JF et al (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408. doi:10.1093/nar/gkm957

    Article  Google Scholar 

  • Wang Y-X, Zuo X, Wang J et al (2010) Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods (San Diego, Calif) 52:180–191. doi:10.1016/j.ymeth.2010.06.009

    Article  Google Scholar 

  • Xia T, SantaLucia J, Burkard ME 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

    Article  Google Scholar 

  • Yedidia JS, Freeman WT, Weiss Y (2005) Constructing free-energy approximations and generalized belief propagation algorithms. IEEE Trans Inf Theory 51:2282–2312. doi:10.1109/TIT.2005.850085

    Article  MathSciNet  Google Scholar 

  • Ying X, Luo H, Luo J, Li W (2004) RDfolder: a web server for prediction of RNA secondary structure. Nucleic Acids Res 32:W150–W153. doi:10.1093/nar/gkh445

    Article  Google Scholar 

  • Zhang Q, Kim N-K, Peterson RD et al (2010) Structurally conserved five nucleotide bulge determines the overall topology of the core domain of human telomerase RNA. Proc Natl Acad Sci USA 107:18761–18768. doi:10.1073/pnas.1013269107

    Article  ADS  Google Scholar 

  • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    Article  Google Scholar 

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Authors and Affiliations

  1. National Magnetic Resonance Facility at Madison, Madison, WI, USA

    Arash Bahrami, Lawrence J. Clos II, John L. Markley & Samuel E. Butcher

  2. Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA

    John L. Markley & Samuel E. Butcher

  3. Department of Molecular and Cellular Physiology, University of Cincinnati, P.O. Box 670576, Cincinnati, OH, 45267-0576, USA

    Hamid R. Eghbalnia

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  1. Arash Bahrami
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  2. Lawrence J. Clos II
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  4. Samuel E. Butcher
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  5. Hamid R. Eghbalnia
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Correspondence to Hamid R. Eghbalnia.

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Arash Bahrami and Lawrence J. Clos contributed equally.

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Bahrami, A., Clos, L.J., Markley, J.L. et al. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts. J Biomol NMR 52, 289–302 (2012). https://doi.org/10.1007/s10858-012-9603-z

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