A general approach to high-yield biosynthesis of chimeric RNAs bearing various types of functional small RNAs for broad applications

Nucleic Acids Research

Volumn 43, Issue 7, 2015, Pages 3857-3869

  Chen, Qiu Xia ^a,b   Wang, Wei Peng ^a   Zeng, Su ^b   Urayama, Shiro ^a   Yu, Ai Ming ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; MESSENGER RNA; MICRORNA; MICRORNA 124; MICRORNA 34A; RIBONUCLEASE; SMALL INTERFERING RNA; TRANSFER RNA; UNTRANSLATED RNA; RNA;

ARTICLE; BACTERIUM CULTURE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE EXPRESSION; GENE TARGETING; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA INTERFERENCE; RNA SEQUENCE; RNA SYNTHESIS; ANIMAL; BIOSYNTHESIS; CONFORMATION; GENE SILENCING; GENETIC RECOMBINATION; GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; TRANSGENIC MOUSE;

BACTERIA (MICROORGANISMS); MUS MUSCULUS;

ANIMALS; BASE SEQUENCE; GENE KNOCKDOWN TECHNIQUES; GREEN FLUORESCENT PROTEINS; MICE; MICE, TRANSGENIC; NUCLEIC ACID CONFORMATION; RECOMBINATION, GENETIC; RNA;

EID: 84930505521     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv228     Document Type: Article

References (40)

1. Dykxhoorn, D.M. and Lieberman, J. (2006) Knocking down disease with siRNAs. Cell, 126, 231-235.
2. Burnett, J.C. and Rossi, J.J. (2012) RNA-based therapeutics: current progress and future prospects. Chem. Biol, 19, 60-71.
3. Kole, R., Krainer, A.R. and Altman, S. (2012) RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat. Rev. Drug Discov., 11, 125-140.
4. Ulrich, H., Trujillo, C.A., Nery, A.A., Alves, J.M., Majumder, P., Resende, R.R. and Martins, A.H. (2006) DNA and RNA aptamers: from tools for basic research towards therapeutic applications. Combinat. Chem. High Throughput Screen., 9, 619-632.
5. Kelnar, K., Peltier, H.J., Leatherbury, N, Stoudemire, J. and Bader, A.G. (2014) Quantifcation of therapeutic miRNA mimics in whole blood from non-human primates. Anal. Chem., 86, 1534-1542.
6. Ling, H., Fabbri, M. and Calin, G.A. (2013) MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nat. Rev. Drug Discov, 12, 847-865.
7. Takahashi, M., Yamada, N, Hatakeyama, H., Murata, M., Sato, Y, Minakawa, N, Harashima, H. and Matsuda, A. (2013) In vitro optimization of 2'-OMe-4'-thioribonucleoside-modifed anti-microRNA oligonucleotides and its targeting delivery to mouse liver using a liposomal nanoparticle. Nucleic Acids Res., 41, 10659-10667.
8. Gebert, L.F., Rebhan, M.A., Crivelli, S.E., Denzler, R., Stoffel, M. and Hall, J. (2014) Miravirsen (SPC3649) can inhibit the biogenesis of miR-122. Nucleic Acids Res., 42, 609-621.
9. Babendure, J.R., Adams, S.R. and Tsien, R.Y. (2003) Aptamers switch on fuorescence of triphenylmethane dyes. J. Am. Chem. Soc., 125, 14716-14717.
10. Beckert, B. and Masquida, B. (2011) Synthesis of RNA by in vitro transcription. Methods Mol Biol, 703, 29-41.
11. Huang, F., He, J., Zhang, Y. and Guo, Y (2008) Synthesis of biotin-AMP conjugate for 5' biotin labeling of RNA through one-step in vitro transcription. Nat. Protoc, 3, 1848-1861.
12. Huang, L., Jin, J., Deighan, P, Kiner, E., McReynolds, L. and Lieberman, J. (2013) Effcient and specifc gene knockdown by small interfering RNAs produced in bacteria. Nat. Biotechnol, 31, 350-356.
13. Ponchon, L. and Dardel, F. (2007) Recombinant RNA technology: the tRNA scaffold. Nat. Methods, 4, 571-576.
14. Ponchon, L., Beauvais, G, Nonin-Lecomte, S. and Dardel, F. (2009) A generic protocol for the expression and purifcation of recombinant RNA in Escherichia coli using a tRNA scaffold. Nat. Protoc, 4, 947-959.
15. Nelissen, F.H., Leunissen, E.H., van de Laar, L., Tessari, M., Heus, H.A. and Wijmenga, S.S. (2012) Fast production of homogeneous recombinant RNA-towards large-scale production of RNA. Nucleic Acids Res., 40, e102.
16. Liu, Y, Stepanov, V.G, Strych, U., Willson, R.C, Jackson, GW. and Fox, GE. (2010) DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli. BMC Biotechnol., 10, 85.
17. Li, M.M., Wang, W.P, Wu, W.J., Huang, M. and Yu, A.M. (2014) Rapid production of novel pre-MicroRNA agent hsa-mir-27b in Escherichia coli using recombinant RNA technology for functional studies in mammalian cells. Drug Metab. Dispos., 42, 1791-1795.
18. Sato, K., Hamada, M., Asai, K. and Mituyama, T. (2009) CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res., 37, W277-W280.
19. Hamada, M., Yamada, K., Sato, K., Frith, M.C. andAsai, K. (2011) CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res., 39, W100-W106.
20. Meyer, C, Grey, F, Kreklywich, CN, Andoh, T.F, Tirabassi, R.S., Orloff, S.L. and Streblow, DN. (2011) Cytomegalovirus microRNA expression is tissue specifc and is associated with persistence. J. Virol, 85, 378-389.
21. Wei, Z., Liu, X., Feng, T. and ChangY. (2011) Novel and conserved micrornas in Dalian purple urchin (Strongylocentrotus nudus) identifed by next generation sequencing. Int. J. Biol. Sci., 7, 180-192.
22. Bi, H.C., Pan, Y.Z., Qiu, J.X., Krausz, K.W., Li, F., Johnson, C.H., Jiang, C.T., Gonzalez, F.J. and Yu, A.M. (2014) N-methylnicotinamide and nicotinamide N-methyltransferase are associated with microRNA-1291-altered pancreatic carcinoma cell metabolome and suppressed tumorigenesis. Carcinogenesis, 35, 2264-2272.
23. Pan, Y.Z., Zhou, A., Hu, Z. and Yu, A.M. (2013) Small nucleolar RNA-derived microRNA hsa-miR-1291 modulates cellular drug disposition through direct targeting of ABC transporter ABCC1. Drug Metab. Dispos., 41, 1744-1751.
24. Okabe, M., Ikawa, M., Kominami, K., Nakanishi, T. and Nishimune, Y. (1997) 'Green mice' as a source of ubiquitous green cells. FEBS Lett., 407, 313-319.
25. Boudreau, R.L. and Davidson, B.L. (2012) Generation of hairpin-based RNAi vectors for biological and therapeutic application. Methods Enzymol., 507, 275-296.
26. Cao, X., Pfaff, S.L. and Gage, F.H. (2007) A functional study of miR-124 in the developing neural tube. Genes Dev., 21, 531-536.
27. Cai, B., Li, J., Wang, J., Luo, X., Ai, J., Liu, Y., Wang, N., Liang, H., Zhang, M., Chen, N. et al. (2012) microRNA-124 regulates cardiomyocyte differentiation of bone marrow-derived mesenchymal stem cells via targeting STAT3 signaling. Stem Cells, 30, 1746-1755.
28. Hatziapostolou, M., Polytarchou, C., Aggelidou, E., Drakaki, A., Poultsides, G.A., Jaeger, S.A., Ogata, H., Karin, M., Struhl, K., Hadzopoulou-Cladaras, M. et al. (2011) An HNF4alpha-miRNA infammatory feedback circuit regulates hepatocellular oncogenesis. Cell, 147, 1233-1247.
29. Reddi, K.K. and Holland, J.F. (1976) Elevated serum ribonuclease in patients with pancreatic cancer. Proc. Natl. Acad. Sci. U.S.A., 73, 2308-2310.
30. Akagi, K., Murai, K., Hirao, N. and Yamanaka, M. (1976) Purifcation and properties of alkaline ribonuclease from human serum. Biochim. Biophys. Acta, 442, 368-378.
31. Gu, S., Jin, L., Zhang, Y, Huang, Y, Zhang, F., Valdmanis, P.N. and Kay, M.A. (2012) The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell, 151, 900-911.
32. Castellano, L. and Stebbing, J. (2013) Deep sequencing of small RNAs identifes canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues. Nucleic Acids Res., 41, 3339-3351.
33. Dueck, A., Ziegler, C, Eichner, A., Berezikov, E. and Meister, G. (2012) microRNAs associated with the different human Argonaute proteins. Nucleic Acids Res., 40, 9850-9862.
34. Kunitz, M. (1950) Crystalline desoxyribonuclease; isolation and general properties; spectrophotometric method for the measurement of desoxyribonuclease activity. J. Gen. Physiol, 33, 349-362.
35. Crook, E.M., Mathias, A.P. and Rabin, B.R. (1960) Spectrophotometric assay of bovine pancreatic ribonuclease by the use of cytidine 2':3'-phosphate. Biochem. J., 74, 234-238.
36. Peterson, L.M. (1979) Serum RNase in the diagnosis of pancreatic carcinoma. Proc. Natl. Acad. Sci. U.S.A., 76, 2630-2634.
37. Potenza, N., Salvatore, V., Migliozzi, A., Martone, V., Nobile, V and Russo, A. (2006) Hybridase activity of human ribonuclease-1 revealed by a real-time fuorometric assay. Nucleic Acids Res, 34, 2906-2913.
38. Kottel, R.H., Hoch, S.O., Parsons, R.G. and Hoch, J.A. (1978) Serum ribonuclease activity in cancer patients. Br. J. Cancer, 38, 280-286.
39. Vlassov, A., Florentz, C, Helm, M., Naumov, V., Buneva, V., Nevinsky, G. and Giege, R. (1998) Characterization and selectivity of catalytic antibodies from human serum with RNase activity. Nucleic Acids Res., 26, 5243-5250.
40. Nakata, D. (2014) Increased N-glycosylation of Asn(8)(8) in serum pancreatic ribonuclease 1 is a novel diagnostic marker for pancreatic cancer. Sci. Rep., 4, 6715.