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PMID: 17611237 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Review

Informatics challenges in structured RNA.

Briefings in bioinformatics ·Vol. 8 ·No. 5 ·2007-09-00 ·Pages 294-303

Laederach A

Abstract

The world of regulatory RNAs is fast expanding into mainstream molecular biology as both a subject of intense mechanistic study and as a tool for functional characterization. The RNA world is one of complex structures that carry out catalysis, sense metabolites and synthesize proteins. The dynamic and structural nature of RNAs presents a whole new set of informatics challenges to the computational community. The ability to relate structure and dynamics to function will be key to understanding this complex world. I review several important classes of structured RNAs that present our community with a series of biologically novel informatics challenges. I also review available informatics tools that have been recently developed in the field.

MeSH Terms
Computational Biology/trends Models, Chemical Models, Molecular Nucleic Acid Conformation RNA/chemistry,genetics,ultrastructure RNA Interference Structure-Activity Relationship
Chemicals
RNA
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Laederach Alain
Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA 94305, USA. alain@helix.stanford.edu
References (65)
65 references, click to expand
  1. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery.
    Nucleic Acids Res. 2004;32(22):6650-9 PMID: 15608296
  2. Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments.
    Nucleic Acids Res. 2005;33(8):2395-409 PMID: 15860776
  3. Illuminating the silence: understanding the structure and function of small RNAs.
    Nat Rev Mol Cell Biol. 2007 Jan;8(1):23-36 PMID: 17183358
  4. Coplanar and coaxial orientations of RNA bases and helices.
    RNA. 2007 May;13(5):643-50 PMID: 17339576
  5. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding.
    Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7045-50 PMID: 17438287
  6. Characterization and identification of microRNA core promoters in four model species.
    PLoS Comput Biol. 2007 Mar 9;3(3):e37 PMID: 17352530
  7. From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements.
    Crit Rev Biochem Mol Biol. 2006 Nov-Dec;41(6):329-38 PMID: 17092822
  8. Rfam: annotating non-coding RNAs in complete genomes.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4 PMID: 15608160
  9. Prediction of functional tertiary interactions and intermolecular interfaces from primary sequence data.
    J Exp Zool B Mol Dev Evol. 2005 Jan 15;304(1):50-63 PMID: 15595717
  10. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.
    RNA. 2005 Mar;11(3):344-54 PMID: 15701734
  11. The application of cluster analysis in the intercomparison of loop structures in RNA.
    RNA. 2005 Apr;11(4):412-23 PMID: 15769871
  12. RNA and protein folding: common themes and variations.
    Biochemistry. 2005 Apr 5;44(13):4957-70 PMID: 15794634
  13. Riboswitches as versatile gene control elements.
    Curr Opin Struct Biol. 2005 Jun;15(3):342-8 PMID: 15919195
  14. Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.
    Bioinformatics. 2005 Aug 1;21(15):3320-1 PMID: 15905274
  15. Describing RNA structure by libraries of clustered nucleotide doublets.
    J Mol Biol. 2005 Aug 5;351(1):26-38 PMID: 15993894
  16. RNA structure: reading the ribosome.
    Science. 2005 Sep 2;309(5740):1508-14 PMID: 16141058
  17. Insights into the mechanisms of splicing: more lessons from the ribosome.
    Genes Dev. 2005 Oct 1;19(19):2255-60 PMID: 16204176
  18. RNAi: RISC gets loaded.
    Cell. 2005 Nov 18;123(4):543-5 PMID: 16286001
  19. An obligate intermediate along the slow folding pathway of a group II intron ribozyme.
    Nucleic Acids Res. 2005;33(21):6674-87 PMID: 16314300
  20. Slicer function of Drosophila Argonautes and its involvement in RISC formation.
    Genes Dev. 2005 Dec 1;19(23):2837-48 PMID: 16287716
  21. Current perspectives in intronic micro RNAs (miRNAs).
    J Biomed Sci. 2006 Jan;13(1):5-15 PMID: 16228283
  22. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins.
    Nucleic Acids Res. 2006;34(6):e48 PMID: 16582097
  23. The RNA Ontology Consortium: an open invitation to the RNA community.
    RNA. 2006 Apr;12(4):533-41 PMID: 16484377
  24. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule.
    J Mol Biol. 2006 May 12;358(4):1179-90 PMID: 16574145
  25. Beyond Mfold: recent advances in RNA bioinformatics.
    J Biotechnol. 2006 Jun 25;124(1):41-55 PMID: 16530285
  26. The building blocks and motifs of RNA architecture.
    Curr Opin Struct Biol. 2006 Jun;16(3):279-87 PMID: 16713707
  27. CONTRAfold: RNA secondary structure prediction without physics-based models.
    Bioinformatics. 2006 Jul 15;22(14):e90-8 PMID: 16873527
  28. The microRNA: overview of the RNA gene that modulates gene functions.
    Methods Mol Biol. 2006;342:1-18 PMID: 16957363
  29. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition.
    Structure. 2006 Sep;14(9):1459-68 PMID: 16962976
  30. Structural motifs in RNA.
    Annu Rev Biochem. 1999;68:287-300 PMID: 10872451
  31. Ribozyme structures and mechanisms.
    Annu Rev Biophys Biomol Struct. 2001;30:457-75 PMID: 11441810
  32. SCOR: a Structural Classification of RNA database.
    Nucleic Acids Res. 2002 Jan 1;30(1):392-4 PMID: 11752346
  33. Exploring the folding landscape of a structured RNA.
    Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):155-60 PMID: 11756689
  34. RNAML: a standard syntax for exchanging RNA information.
    RNA. 2002 Jun;8(6):707-17 PMID: 12088144
  35. The non-Watson-Crick base pairs and their associated isostericity matrices.
    Nucleic Acids Res. 2002 Aug 15;30(16):3497-531 PMID: 12177293
  36. Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules.
    Biochimie. 2002 Sep;84(9):961-73 PMID: 12458088
  37. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting".
    Curr Opin Struct Biol. 2002 Oct;12(5):648-53 PMID: 12464318
  38. Rfam: an RNA family database.
    Nucleic Acids Res. 2003 Jan 1;31(1):439-41 PMID: 12520045
  39. The nucleic acid database.
    Methods Biochem Anal. 2003;44:199-216 PMID: 12688301
  40. Tools for the automatic identification and classification of RNA base pairs.
    Nucleic Acids Res. 2003 Jul 1;31(13):3450-60 PMID: 12824344
  41. Analysis of RNA motifs.
    Curr Opin Struct Biol. 2003 Jun;13(3):300-8 PMID: 12831880
  42. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
    Nucleic Acids Res. 2003 Aug 15;31(16):4755-61 PMID: 12907716
  43. RNA backbone is rotameric.
    Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13904-9 PMID: 14612579
  44. SCOR: Structural Classification of RNA, version 2.0.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D182-4 PMID: 14681389
  45. Recognition of small interfering RNA by a viral suppressor of RNA silencing.
    Nature. 2003 Dec 18;426(6968):874-8 PMID: 14661029
  46. Computational identification of microRNAs and their targets.
    Comput Biol Chem. 2006 Dec;30(6):395-407 PMID: 17123865
  47. Detection of the argonaute protein Ago2 and microRNAs in the RNA induced silencing complex (RISC) using a monoclonal antibody.
    J Immunol Methods. 2006 Dec 20;317(1-2):38-44 PMID: 17054975
  48. High-throughput method for the prediction of low-resolution, three-dimensional RNA structures.
    Nucleic Acids Symp Ser (Oxf). 2006;(50):67-8 PMID: 17150820
  49. The interaction networks of structured RNAs.
    Nucleic Acids Res. 2006;34(22):6587-604 PMID: 17135184
  50. Does native state topology determine the RNA folding mechanism?
    J Mol Biol. 2004 Apr 2;337(4):789-97 PMID: 15033351
  51. Theory of protein folding.
    Curr Opin Struct Biol. 2004 Feb;14(1):70-5 PMID: 15102452
  52. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
    Nucleic Acids Res. 2004;32(8):2342-52 PMID: 15121895
  53. Reduced contact order and RNA folding rates.
    J Mol Biol. 2004 Oct 1;342(5):1359-65 PMID: 15364565
  54. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme.
    J Mol Biol. 2004 Oct 1;342(5):1431-42 PMID: 15364572
  55. Quantitative DNase footprint titration: a method for studying protein-DNA interactions.
    Methods Enzymol. 1986;130:132-81 PMID: 3773731
  56. "Footprint" titrations yield valid thermodynamic isotherms.
    Proc Natl Acad Sci U S A. 1986 Nov;83(22):8462-6 PMID: 3464963
  57. Defining the inside and outside of a catalytic RNA molecule.
    Science. 1989 Jul 21;245(4915):276-82 PMID: 2501870
  58. Hints of a language in junk DNA.
    Science. 1994 Nov 25;266(5189):1320 PMID: 7973718
  59. Helical stacking in DNA three-way junctions containing two unpaired pyrimidines: proton NMR studies.
    Biophys J. 1995 Jan;68(1):251-65 PMID: 7711249
  60. Crystal structure of a group I ribozyme domain: principles of RNA packing.
    Science. 1996 Sep 20;273(5282):1678-85 PMID: 8781224
  61. Linguistic features of noncoding DNA sequences.
    Phys Rev Lett. 1994 Dec 5;73(23):3169-72 PMID: 10057305
  62. Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics.
    Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1995 Sep;52(3):2939-50 PMID: 9963739
  63. Hydroxyl radical footprinting of DNA complexes of the ets domain of PU.1 and its comparison to the crystal structure.
    Biochemistry. 1998 Apr 14;37(15):5129-35 PMID: 9548743
  64. Statistical properties of DNA sequences.
    Physica A. 1995;221:180-92 PMID: 11540495
  65. Strategies for RNA folding and assembly.
    Nat Rev Mol Cell Biol. 2004 Nov;5(11):908-19 PMID: 15520810
Article Info
Journal
Briefings in bioinformatics
Abbr.
Brief Bioinform
ISSN
1477-4054
DOI
10.1093/bib/bbm026
Email
alain@helix.stanford.edu
Published
2007-09-00
Epub
2007-00-04
Pages
294-303
Language
English
Region
England
NLM ID
100912837
PMCID
PMC2629073
Subset
IM
Grants
NIGMS NIH HHS · P01 GM66275 · United States
NCRR NIH HHS · P41 RR006009-177600 · United States
NIGMS NIH HHS · K99 GM079953 · United States
NIGMS NIH HHS · K99-GM079953 · United States
NCRR NIH HHS · P41 RR006009-185497 · United States
NCRR NIH HHS · P41 RR006009 · United States
NIGMS NIH HHS · U54 GM072970 · United States
NIGMS NIH HHS · P01 GM066275 · United States
External Links
PubMed source DOI: 10.1093/bib/bbm026 PMC Full Text View journal details
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