Predictions of protein-RNA interactions

Wiley Interdisciplinary Reviews: Computational Molecular Science

Volumn 3, Issue 2, 2013, Pages 161-175

  Cirillo, Davide ^a   Agostini, Federico ^a   Tartaglia, Gian Gaetano ^a  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR PROCESS; HIGH THROUGHPUT EXPERIMENTS; HOST DEFENSE; INTERACTION NETWORKS; POST-TRANSCRIPTIONAL REGULATIONS; PROTEIN-RNA INTERACTION; RIBONUCLEOPROTEINS; RNA MOLECULES; RNA-PROTEIN INTERACTIONS;

GENE EXPRESSION; RNA;

PROTEINS;

EID: 84873723387     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1119     Document Type: Review

References (63)

1. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
2. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
3. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol 2006, 7(suppl 1):S4.1-9.
4. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
5. Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011, 43:904-914.
6. Khalil AM, Rinn JL. RNA-protein interactions in human health and disease. Semin Cell Dev Biol 2011, 22:359-365.
7. Chen Y, Varani G. Protein families and RNA recognition. FEBS J 2005, 272:2088-2097.
8. Glisovic T, Bachorik JL, Yong J, Dreyfuss G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 2008, 582:1977-1986.
9. Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 2002, 30:1427-1464.
10. Cammer S, Carter CW Jr. Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase. Bioinformatics 2010, 26:709-714.
11. Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 2011, 40:D302-D305.
12. Stawiski EW, Gregoret LM, Mandel-Gutfreund Y. Annotating nucleic acid-binding function based on protein structure. J Mol Biol 2003, 326:1065-1079.
13. Bellucci M, Agostini F, Masin M, Tartaglia GG. Predicting protein associations with long noncoding RNAs. Nat Methods 2011, 8:444-445.
14. Goodrich JA, Kugel JF. Non-coding-RNA regulators of RNA polymerase II transcription. Nat Rev Mol Cell Biol 2006, 7:612-616.
15. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
16. Lundblad EW, Altman S. Inhibition of gene expression by RNase P. N Biotechnol 2010, 27:212-221.
17. Sakano H, Yamada S, Ikemura T, Shimura Y, Ozeki H. Temperature sensitive mutants of Escherichia coli for tRNA synthesis. Nucleic Acids Res 1974, 1:355-371.
18. Koutmou KS, Zahler NH, Kurz JC, Campbell FE, Harris ME, Fierke CA. Protein-precursor tRNA contact leads to sequence-specific recognition of 5′ leaders by bacterial ribonuclease P. J Mol Biol 2010, 396:195-208.
19. Koutmou KS, Zahler NH, Kurz JC, Campbell FE, Harris ME, Fierke CA. Protein-precursor tRNA contact leads to sequence-specific recognition of 5′ leaders by bacterial ribonuclease P. J Mol Biol 2010, 396:195-208.
20. Romeo T, Gong M. Genetic and physical mapping of the regulatory gene csrA on the Escherichia coli K-12 chromosome. J Bacteriol 1993, 175:5740-5741.
21. Liu MY, Yang H, Romeo T. The product of the pleiotropic Escherichia coli gene csrA modulates glycogen biosynthesis via effects on mRNA stability. J Bacteriol 1995, 177:2663-2672.
22. Liu MY, Romeo T. The global regulator CsrA of Escherichia coli is a specific mRNA-binding protein. J Bacteriol 1997, 179:4639-4642.
23. Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yüksel U, Giedroc DP, Romeo T. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 1997, 272:17502-17510.
24. Muppirala UK, Honavar VG, Dobbs D. Predicting RNA-protein interactions using only sequence information. BMC Bioinformatics 2011, 12:489.
25. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. The Vienna RNA Websuite. Nucleic Acids Res 2008, 36:W70-W74.
26. Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 1978, 47:45-148.
27. Deléage G, Roux B. An algorithm for protein secondary structure prediction based on class prediction. Protein Eng 1987, 1:289-294.
28. Morozova N, Allers J, Myers J, Shamoo Y. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. Bioinformatics 2006, 22:2746-2752.
29. Grantham R. Amino acid difference formula to help explain protein evolution. Science 1974, 185:862-864.
30. Zimmerman JM, Eliezer N, Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 1968, 21, 170-201.
31. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982, 157:105-132.
32. Bull HB, Breese K. Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues. Arch Biochem Biophys 1974, 161:665-670.
33. Wu T, Wang J, Liu C, Zhang Y, Shi B, Zhu X, Zhang Z, Skogerbø G, Chen L, Lu H, Zhao Y, Chen R. NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nucleic Acids Res 2006, 34:D150-D152.
34. Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S. Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics 2011, 12(suppl 13):S5.
35. Kumar M, Gromiha MM, Raghava GPS. SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. J Mol Recognit 2011, 24:303-313.
36. Wang Y, Xue Z, Shen G, Xu J. PRINTR: prediction of RNA binding sites in proteins using SVM and profiles. Amino Acids 2008, 35:295-302.
37. Terribilini M, Sander JD, Lee J-H, Zaback P, Jernigan RL, Honavar V, Dobbs D. RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res 2007, 35:W578-W584.
38. Liu T, Geng X, Zheng X, Li R, Wang J. Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles. Amino Acids 2012, 42:2243-2249.
39. Towfic F, Caragea C, Gemperline DC, Dobbs D, Honavar V. Struct-NB: predicting protein-RNA binding sites using structural features. Int J Data Min Bioinform 2010, 4:21-43.
40. Maetschke SR, Yuan Z. Exploiting structural and topological information to improve prediction of RNA-protein binding sites. BMC Bioinformatics 2009, 10:341.
41. Shazman S, Mandel-Gutfreund Y. Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput Biol 2008, 4:e1000146.
42. Zhao H, Yang Y, Zhou Y. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction. RNA Biol 2011, 8:988-996.
43. Pérez-Cano L, Fernández-Recio J. Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins. Proteins 2010, 78:25-35.
44. Sweet RM, Eisenberg D. Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol 1983, 171:479-488.
45. Wang G, Dunbrack RL Jr. PISCES: a protein sequence culling server. Bioinformatics 2003, 19:1589-1591.
46. Allers J, Shamoo Y. Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J Mol Biol 2001, 311:75-86.
47. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994, 3:522-524.
48. Lensink MF, Wodak SJ. Docking and scoring protein interactions: CAPRI 2009. Proteins 2010, 78:3073-3084.
49. Cheng TM-K, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007, 68:503-515.
50. Gherghe CM, Leonard CW, Ding F, Dokholyan NV, Weeks KM. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc 2009, 131:2541-2546.
51. Cruz JA, Blanchet M-F, Boniecki M, Bujnicki JM, Chen S-J, Cao S, Das R, et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA 2012.
52. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, et al. PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 2010.
53. Ke A, Doudna JA. Crystallization of RNA and RNA-protein complexes. Methods 2004, 34:408-414.
54. Wu H, Finger LD, Feigon J. Structure determination of protein/RNA complexes by NMR. Meth Enzymol 2005, 394:525-545.
55. Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc Natl Acad Sci USA 2008, 105:4144-4149.
56. Mertens HDT, Svergun DI. Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 2010, 172:128-141.
57. Jurica MS. Detailed close-ups and the big picture of spliceosomes. Curr Opin Struct Biol 2008, 18:315-320.
58. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149:1393-1406.
59. Weeks KM. Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol 2010, 20:295-304.
60. Lipfert J, Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 2007, 36:307-327.
61. Ding F, Lavender CA, Weeks KM, Dokholyan NV. Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods 2012.
62. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci 2009, 106:11667-11672.
63. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983, 35:849-857.