Tertiary structure-based analysis of microRNA-target interactions

RNA

Volumn 19, Issue 4, 2013, Pages 539-551

  Gan, Hin Hark ^a   Gunsalus, Kristin C ^a,b  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

Author keywords

Duplex binding free energy; Entropy of duplex formation; microRNA; miRNA tertiary structures; miRNA Argonaute docking

Indexed keywords

ARGONAUTE PROTEIN; DOUBLE STRANDED RNA; MICRORNA; SINGLE STRANDED RNA;

ARTICLE; BINDING AFFINITY; CAENORHABDITIS ELEGANS; CALORIMETRY; ENTROPY; IONIC STRENGTH; MOLECULAR INTERACTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PREDICTION; PRIORITY JOURNAL; RNA HYBRIDIZATION; RNA STRUCTURE;

ANIMALS; ARGONAUTE PROTEINS; CAENORHABDITIS ELEGANS; ENERGY METABOLISM; MICRORNAS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA, HELMINTH; THERMUS THERMOPHILUS;

CAENORHABDITIS ELEGANS;

EID: 84875466989     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.035691.112     Document Type: Article

References (56)

1. Abu Almakarem AS, Petrov AI, Stombaugh J, Zirbel CL, Leontis NB. 2012. Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res 40: 1407-1423.
2. Ambros V. 2004. The functions of animal microRNAs. Nature 431: 350-355.
3. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci 98: 10037-10041.
4. Balasubramanian C, Ojha RP, Maiti S, Desideri A. 2010. Sampling the structure of the noncanonical lin-4:lin-14 microRNA:mRNA complex by molecular dynamics simulations. J Phys Chem B 114: 16443-16449.
5. Bartel DP. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136: 215-233.
6. Bashford D, Case DA. 2000. Generalized Born models of macromolecular solvation effects. Annu Rev Phys Chem 51: 129-152.
7. Boland A, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O. 2011. Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein. Proc Natl Acad Sci 108: 10466-10471.
8. Brennecke J, Stark A, Russell RB, Cohen SM. 2005. Principles of microRNA-target recognition. PLoS Biol 3: e85.
9. Cao S, Chen SJ. 2011. Physics-based de novo prediction of RNA 3D structures. J Phys Chem B 115: 4216-4226.
10. Cao S, Chen SJ. 2012. Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Res 40: 4681-4690.
11. Cevec M, Thibaudeau C, Plavec J. 2008. Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans. Nucleic Acids Res 36: 2330-2337.
12. Cevec M, Thibaudeau C, Plavec J. 2010. NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans. Nucleic Acids Res 38: 7814-7821.
13. Chi SW, Zang JB, Mele A, Darnell RB. 2009. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
14. Chi SW, Hannon GJ, Darnell RB. 2012. An alternative mode of microRNA target recognition. Nat Struct Mol Biol 19: 321-327.
15. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117: 5179-5197.
16. Das R, Baker D. 2007. Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci 104: 14664-14669.
17. Das R, Baker D. 2008. Macromolecular modeling with rosetta. Annu Rev Biochem 77: 363-382.
18. Das R, Karanicolas J, Baker D. 2010. Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods 7: 291-294.
19. Didiano D, Hobert O. 2008. Molecular architecture of a miRNA-regulated 3′ UTR. RNA 14: 1297-1317.
20. Dill KA. 1997. Additivity principles in biochemistry. J Biol Chem 272: 701-704.
21. Dong F, Olsen B, Baker NA. 2008. Computational methods for biomolecular electrostatics. Methods Cell Biol 84: 843-870.
22. Farh KK, Grimson A, Jan C, Lewis BP, Johnston WK, Lim LP, Burge CB, Bartel DP. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817-1821.
23. Fennell CJ, Kehoe CW, Dill KA. 2011. Modeling aqueous solvation with semi-explicit assembly. Proc Natl Acad Sci 108: 3234-3239.
24. Friedman RC, Farh KK, Burge CB, Bartel DP. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92- 105.
25. Grun D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N. 2005. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1: e13.
26. Hammell M, Long D, Zhang L, Lee A, Carmack CS, Han M, Ding Y, Ambros V. 2008. mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods 5: 813-819.
27. Hofacker IL. 2003. Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
28. Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. 2009. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15: 189-199.
29. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. 2007. The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
30. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, et al. 2000. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
31. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, Macmenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. 2005. Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
32. Lall S,GrunD,Krek A,ChenK,WangYL,DeweyCN,SoodP,ColomboT, BrayN,MacmenaminP, et al. 2006.Agenome-widemapof conserved microRNA targets in C. elegans. Curr Biol 16: 460-471.
33. Leach AR. 1996. Molecular modeling: Principles and applications. Addison Wesley Longman, Singapore.
34. Liu L, Chen SJ. 2010. Computing the conformational entropy for RNA folds. J Chem Phys 132: 235104.
35. Lodish H, Beck A, Zipursky S, Matsudaira P, Baltimore D, Darnell J. 2000. Molecular cell biology. Freeman, New York.
36. McColl G, James SA, Mayo S, Howard DL, Ryan CG, Kirkham R, Moorhead GF, Paterson D, de Jonge MD, Bush AI. 2012. Caenorhabditis elegans maintains highly compartmentalized cellular distribution of metals and steep concentration gradients of manganese. PLoS ONE 7: e32685.
37. Nakanishi K, Weinberg DE, Bartel DP, Patel DJ. 2012. Structure of yeast Argonaute with guide RNA. Nature 486: 368-374.
38. Paciello G, Acquaviva A, Ficarra E, Deriu MA, Macii E. 2011. A molecular dynamics study of a miRNA:mRNA interaction. J Mol Model 17: 2895-2906.
39. Pappu RV, Hart RK, Ponder JW. 1998. Analysis and application of potential energy smoothing and search methods for global optimization. J Phys Chem B 102: 9725-9742.
40. Parisien M, Major F. 2008. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452: 51-55.
41. Parker JS, Parizotto EA, Wang M, Roe SM, Barford D. 2009. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/ MID domain protein. Mol Cell 33: 204-214.
42. Rocchia W, Alexov E, Honig B. 2001. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J Phys Chem B 105: 6507-6514.
43. Roux B, Simonson T. 1999. Implicit solvent models. Biophys Chem 78: 1-20.
44. Sethupathy P, Corda B, Hatzigeorgiou AG. 2006. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12: 192-197.
45. Srinivasan J, Miller J, Kollman PA, Case DA. 1998. Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn 16: 671-682.
46. Tidor B, Karplus M. 1994. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J Mol Biol 238: 405-414.
47. Vella MC, Reinert K, Slack FJ. 2004. Architecture of a validated microRNA::target interaction. Chem Biol 11: 1619-1623.
48. Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel DJ. 2008a. Structure of an Argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456: 921-926.
49. Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ. 2008b. Structure of the guide-strand-containing Argonaute silencing complex. Nature 456: 209-213.
50. Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ. 2009. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461: 754-761.
51. Wang Y, Li Y, Ma Z, YangW, Ai C. 2010. Mechanism of microRNA-target interaction: Molecular dynamics simulations and thermodynamics analysis. PLoS Comput Biol 6: e1000866.
52. Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH. 1998. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
53. Xin Y, Olson WK. 2009. BPS: A database of RNA base-pair structures. Nucleic Acids Res 37: D83-D88.
54. Xu B, Shen H, Zhu X, Li G. 2011. Fast and accurate computation schemes for evaluating vibrational entropy of proteins. J Comput Chem 32: 3188-3193.
55. Zhang L, Hammell M, Kudlow BA, Ambros V, Han M. 2009. Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development 136: 3043-3055.
56. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW. 2010. Comprehensive discovery of endogenous Argonaute binding sites inCaenorhabditis elegans.Nat StructMol Biol 17: 173-179.