High-throughput assay and engineering of self-cleaving ribozymes by sequencing

Nucleic Acids Research

Volumn 43, Issue 13, 2015, Pages e85-

  Kobori, Shungo ^a   Nomura, Yoko ^a   Miu, Anh ^a   Yokobayashi, Yohei ^a,b  

^a University of California   (United States)

^b OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME; SELF CLEAVING RIBOZYME; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; ENZYME ENGINEERING; GENE SWITCHING; HEK293 CELL LINE; HIGH THROUGHPUT SEQUENCING; PRIORITY JOURNAL; REPORTER GENE; ALLOSTERISM; CHEMISTRY; DNA SEQUENCE; GENE LIBRARY; GENETIC ENGINEERING; HUMAN; METABOLISM; PROCEDURES; RNA CLEAVAGE;

ALLOSTERIC REGULATION; GENE LIBRARY; GENETIC ENGINEERING; HEK293 CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RNA CLEAVAGE; RNA, CATALYTIC; SEQUENCE ANALYSIS, DNA;

EID: 84939618118     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv265     Document Type: Article

References (30)

1. Webb,C.H., Riccitelli,N.J., Ruminski,D.J. and Lupták,A. (2009) Widespread occurrence of self-cleaving ribozymes. Science, 326, 953.
2. Webb,C.H. and Lupták,A. (2011) HDV-like self-cleaving ribozymes. RNA Biol., 8, 719-727.
3. Roth,A., Weinberg,Z., Chen,A.G., Kim,P.B., Ames,T.D. and Breaker,R.R. (2014) A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat. Chem. Biol., 10, 56-60.
4. Hammann,C., Lupták,A., Perreault,J. and de la Peña,M. (2012) The ubiquitous hammerhead ribozyme. RNA, 18, 871-885.
5. Chen,X., Li,N. and Ellington,A.D. (2007) Ribozyme catalysis of metabolism in the RNA world. Chem. Biodivers., 4, 633-655.
6. Ellington,A.D. and Szostak,J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
7. Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
8. Frommer,J., Appel,B. and Müller,S. (2015) Ribozymes that can be regulated by external stimuli. Curr. Opin. Biotechnol., 31, 35-41.
9. Wittmann,A. and Suess,B. (2012) Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett., 586, 2076-2083.
10. Eiler,D., Wang,J. and Steitz,T.A. (2014) Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proc. Natl. Acad. Sci. U.S.A., 111, 13028-13033.
11. Liu,Y., Wilson,T.J., McPhee,S.A. and Lilley,D.M. (2014) Crystal structure and mechanistic investigation of the twister ribozyme. Nat. Chem. Biol., 10, 739-744.
12. Nomura,Y., Zhou,L., Miu,A. and Yokobayashi,Y. (2013) Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth. Biol., 2, 684-689.
13. Kumar,D., An,C.I. and Yokobayashi,Y. (2009) Conditional RNA interference mediated by allosteric ribozyme. J. Am. Chem. Soc., 131, 13906-13907.
14. Mandal,M., Boese,B., Barrick,J.E., Winkler,W.C. and Breaker,R.R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell, 113, 577-586.
15. Thill,G., Vasseur,M. and Tanner,N.K. (1993) Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme. Biochemistry, 32, 4254-4262.
16. Breaker,R.R. (2002) Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol., 13, 31-39.
17. Soukup,G.A. and Breaker,R.R. (2000) Allosteric nucleic acid catalysts. Curr. Opin. Struct. Biol., 10, 318-325.
18. Beier,R., Pahlke,C., Quenzel,P., Henseleit,A., Boschke,E., Cuniberti,G. and Labudde,D. (2014) Selection of a DNA aptamer against norovirus capsid protein VP1. FEMS Microbiol. Lett., 351, 162-169.
19. Cho,M., Oh,S.S., Nie,J., Stewart,R., Eisenstein,M., Chambers,J., Marth,J.D., Walker,F., Thomson,J.A. and Soh,H.T. (2013) Quantitative selection and parallel characterization of aptamers. Proc. Natl. Acad. Sci. U.S.A., 110, 18460-18465.
20. Ditzler,M.A., Lange,M.J., Bose,D., Bottoms,C.A., Virkler,K.F., Sawyer,A.W., Whatley,A.S., Spollen,W., Givan,S.A. and Burke,D.H. (2013) High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res., 41, 1873-1884.
21. Hoon,S., Zhou,B., Janda,K.D., Brenner,S. and Scolnick,J. (2011) Aptamer selection by high-throughput sequencing and informatic analysis. Biotechniques, 51, 413-416.
22. Jiménez,J.I., Xulvi-Brunet,R., Campbell,G.W., Turk-MacLeod,R. and Chen,I.A. (2013) Comprehensive experimental fitness landscape and evolutionary network for small RNA. Proc. Natl. Acad. Sci. U.S.A., 110, 14984-14989.
23. Kupakuwana,G.V., Crill,J.E. II, McPike,M.P. and Borer,P.N. (2011) Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing. PLoS ONE, 6, e19395.
24. Schütze,T., Wilhelm,B., Greiner,N., Braun,H., Peter,F., Mörl,M., Erdmann,V.A., Lehrach,H., Konthur,Z., Menger,M. et al. (2011) Probing the SELEX Process with Next-Generation Sequencing. PLoS ONE, 6, e29604.
25. Tome,J.M., Ozer,A., Pagano,J.M., Gheba,D., Schroth,G.P. and Lis,J.T. (2014) Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. Nat. Methods, 11, 683-688.
26. Wilson,R., Bourne,C., Chaudhuri,R.R., Gregory,R., Kenny,J. and Cossins,A. (2014) Single-step selection of bivalent aptamers validated by comparison with SELEX using high-throughput sequencing. PLoS ONE, 9, e100572.
27. Pitt,J.N. and Ferré-D'Amaré,A.R. (2010) Rapid construction of empirical RNA fitness landscapes. Science, 330, 376-379.
28. Ameta,S., Winz,M.L., Previti,C. and Jäschke,A. (2014) Next-generation sequencing reveals how RNA catalysts evolve from random space. Nucleic Acids Res., 42, 1303-1310.
29. Schlosser,K., Lam,J.C. and Li,Y. (2009) A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype. Nucleic Acids Res., 37, 3545-3557.
30. Hafner,M., Renwick,N., Farazi,T.A., Mihailovic,A., Pena,J.T. and Tuschl,T. (2012) Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing. Methods, 58, 164-170.