Current perspectives on RNA secondary structure probing

Biochemical Society Transactions

Volumn 42, Issue 4, 2014, Pages 1251-1255

  Kenyon, Julia ^a   Prestwood, Liam ^a   Lever, Andrew ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Nucleotide; RNA structure; Selective 2' hydroxy acylation analysed by primer extension (SHAPE); Structural analysis

Indexed keywords

RNA;

ACCURACY; ACYLATION; CAPILLARY ELECTROPHORESIS; CONFERENCE PAPER; CYTOPLASM; ELECTROPHORETIC MOBILITY; GEL ELECTROPHORESIS; NUCLEOPHILICITY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RADIOACTIVITY; REPRODUCIBILITY; REVERSE TRANSCRIPTION; RNA ANALYSIS; RNA CONFORMATION; RNA STRUCTURE; X RAY CRYSTALLOGRAPHY; ALGORITHM; ANIMAL; BIOLOGY; CHEMISTRY; CONFORMATION; HUMAN;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; HUMANS; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RNA;

EID: 84905851719     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20140084     Document Type: Conference Paper

References (37)

1. Li, F., Zheng, Q., Ryvkin, P., Dragomir, I., Desai, Y., Aiyer, S., Valladares, O., Yang, J., Bambina, S., Sabin, L.R. et al. (2012) Global analysis of RNA secondary structure in two metazoans. Cell Rep. 1, 69-82
2. Buratti, E. and Baralle, F.E. (2004) Influence of RNA secondary structure on the pre-mRNA splicing process. Mol. Cell. Biol. 24, 10505-10514
3. Garst, A.D., Edwards, A.L. and Batey, R.T. (2011) Riboswitches: structures and mechanisms. Cold Spring Harb. Perspect. Biol. 3, a003533
4. Ziehler, W.A. and Engelke, D.R. (2001) Probing RNA structure with chemical reagents and enzymes. Curr. Protoc. Nucleic Acid Chem. Chapter 6, Unit 6.1
5. Kenyon, J.C., Ghazawi, A., Cheung, W.K., Phillip, P.S., Rizvi, T.A. and Lever, A.M. (2008) The secondary structure of the 5 end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop. RNA 14, 2597-2608
6. Lindell, M., Romby, P. and Wagner, E.G. (2002) Lead(II) as a probe for investigating RNA structure in vivo. RNA 8, 534-541
7. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415
8. Reuter, J.S. and Mathews, D.H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11, 129
9. Merino, E.J., Wilkinson, K.A., Coughlan, J.L. and Weeks, K.M. (2005) RNA structure analysis at single nucleotide resolution by selective 2-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223-4231
10. Wilkinson, K.A., Gorelick, R.J., Vasa, S.M., Guex, N., Rein, A., Mathews, D.H., Giddings, M.C. and Weeks, K.M. (2008) High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol. 6, e96
11. Mitra, S., Shcherbakova, I.V., Altman, R.B., Brenowitz, M. and Laederach, A. (2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. 36, e63
12. Novikova, I.V., Hennelly, S.P. and Sanbonmatsu, K.Y. (2012) Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res. 40, 5034-5051
13. Vasa, S.M., Guex, N., Wilkinson, K.A., Weeks, K.M. and Giddings, M.C. (2008) ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14, 1979-1990
14. McGinnis, J.L., Dunkle, J.A., Cate, J.H. and Weeks, K.M. (2012) The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc. 134, 6617-6624
15. Wilkinson, K.A., Vasa, S.M., Deigan, K.E., Mortimer, S.A., Giddings, M.C. and Weeks, K.M. (2009) Influence of nucleotide identity on ribose 2-hydroxyl reactivity in RNA. RNA 15, 1314-1321
16. Kenyon, J.C., Tanner, S.J., Legiewicz, M., Phillip, P.S., Rizvi, T.A., Le Grice, S.F. and Lever, A.M. (2011) SHAPE analysis of the FIV leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization. Nucleic Acids Res. 39, 6692-6704
17. Clever, J., Sassetti, C. and Parslow, T.G. (1995) RNA secondary structure and binding sites for gag gene products in the 5 packaging signal of human immunodeficiency virus type 1. J. Virol. 69, 2101-2109
18. Berkhout, B. and van Wamel, J.L. (2000) The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure. RNA 6, 282-295
19. Abbink, T.E. and Berkhout, B. (2003) A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon. J. Biol. Chem. 278, 11601-11611
20. Harrison, G.P. and Lever, A.M. (1992) The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure. J. Virol. 66, 4144-4153
21. Lu, K., Heng, X., Garyu, L., Monti, S., Garcia, E.L., Kharytonchyk, S., Dorjsuren, B., Kulandaivel, G., Jones, S., Hiremath, A. et al. (2011) NMR detection of structures in the HIV-1 5-leader RNA that regulate genome packaging. Science 334, 242-245
22. Edwards, T.E., Klein, D.J. and Ferre-D'Amare, A.R. (2007) Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr. Opin. Struct. Biol. 17, 273-279
23. Abbink, T.E., Ooms, M., Haasnoot, P.C. and Berkhout, B. (2005) The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation. Biochemistry 44, 9058-9066
24. Kenyon, J.C., Prestwood, L.J., Le Grice, S.F. and Lever, A.M. (2013) In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader. Nucleic Acids Res. 41, e174
25. Steen, K.A., Rice, G.M. and Weeks, K.M. (2012) Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J. Am. Chem. Soc. 134, 13160-13163
26. Stephenson, J.D., Li, H., Kenyon, J.C., Symmons, M., Klenerman, D. and Lever, A.M. (2013) Three-dimensional RNA structure of the major HIV-1 packaging signal region. Structure 21, 951-962
27. Gherghe, C.M., Leonard, C.W., Ding, F., Dokholyan, N.V. and Weeks, K.M. (2009) Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J. Am. Chem. Soc. 131, 2541-2546
28. Wan, Y., Qu, K., Zhang, Q.C., Flynn, R.A., Manor, O., Ouyang, Z., Zhang, J., Spitale, R.C., Snyder, M.P., Segal, E. et al. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706-709
29. Underwood, J.G., Uzilov, A.V., Katzman, S., Onodera, C.S., Mainzer, J.E., Mathews, D.H., Lowe, T.M., Salama, S.R. and Haussler, D. (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods 7, 995-1001
30. Kertesz, M., Wan, Y., Mazor, E., Rinn, J.L., Nutter, R.C., Chang, H.Y. and Segal, E. (2010) Genome-wide measurement of RNA secondary structure in yeast. Nature 467, 103-107
31. Ding, Y., Tang, Y., Kwok, C.K., Zhang, Y., Bevilacqua, P.C. and Assmann, S.M. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505, 696-700
32. Lucks, J.B., Mortimer, S.A., Trapnell, C., Luo, S., Aviran, S., Schroth, G.P., Pachter, L., Doudna, J.A. and Arkin, A.P. (2011) Multiplexed RNA structure characterization with selective 2-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc. Natl. Acad. Sci. U.S.A. 108, 11063-11068
33. Kielpinski, L.J. and Vinther, J. (2014) Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res. 42, e70
34. Spitale, R.C., Crisalli, P., Flynn, R.A., Torre, E.A., Kool, E.T. and Chang, H.Y. (2013) RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9, 18-20
35. Kwok, C.K., Ding, Y., Tang, Y., Assmann, S.M. and Bevilacqua, P.C. (2013) Determination of in vivo RNA structure in low-abundance transcripts. Nat. Commun. 4, 2971
36. Thurner, C., Witwer, C., Hofacker, I.L. and Stadler, P.F. (2004) Conserved RNA secondary structures in Flaviviridae genomes. J. Gen. Virol. 85, 1113-1124
37. Hajdin, C.E., Bellaousov, S., Huggins, W., Leonard, C.W., Mathews, D.H. and Weeks, K.M. (2013) Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc. Natl. Acad. Sci. U.S.A. 110, 5498-5503