Effects of different target sites on antisense RNA-mediated regulation of gene expression |
Park, Hongmarn
(Department of Chemistry, KAIST)
Yoon, Yeongseong (Korea Science Academy of KAIST) Suk, Shinae (Department of Chemistry, KAIST) Lee, Ji Young (Department of Chemistry, KAIST) Lee, Younghoon (Department of Chemistry, KAIST) |
1 | Rasmussen, A. A., Eriksen, M., Gilany, K., Udesen, C., Franch, T., Petersen, C. and Valentin-Hansen, P. (2005) Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control. Mol. Microbiol. 58, 1421-1429. DOI ScienceOn |
2 | Afonyushkin, T., Vecerek, B., Moll, I., Blasi, U. and Kaberdin, V. R. (2005) Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Res. 33, 1678-1689. DOI ScienceOn |
3 | Mandin, P. and Gottesman, S. (2010) Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J. 29, 3094-3107. DOI ScienceOn |
4 | Vogel, J., Argaman, L., Wagner, E. G. and Altuvia, S. (2004) The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr. Biol. 14, 2271-2276. DOI ScienceOn |
5 | Chen, S., Zhang, A., Blyn, L. B. and Storz, G. (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J. Bacteriol. 186, 6689-6697. DOI ScienceOn |
6 | Overgaard, M., Johansen, J., Moller-Jensen, J. and Valentin-Hansen, P. (2009) Switching off small RNA regulation with trap-mRNA. Mol. Microbiol. 73, 790-800. DOI ScienceOn |
7 | Geissmann, T. A. and Touati, D. (2004) Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator. EMBO J. 23, 396-405. DOI ScienceOn |
8 | Sharma, C. M., Darfeuille, F., Plantinga, T. H. and Vogel, J. (2007) A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev. 21, 2804-2817. DOI ScienceOn |
9 | Bouvier, M., Sharma, C. M., Mika, F., Nierhaus, K. H. and Vogel, J. (2008) Small RNA binding to 5' mRNA coding region inhibits translational initiation. Mol. Cell 32, 827-837. DOI ScienceOn |
10 | Kim, Y. and Lee, Y. (2009) Novel function of C5 protein as a metabolic stabilizer of M1 RNA. FEBS Lett. 583, 419-424. DOI ScienceOn |
11 | Kim, S., Kim, H., Park, I. and Lee, Y. (1996) Mutational analysis of RNA structures and sequences postulated to affect 3' processing of M1 RNA, the RNA component of Escherichia coli RNase P. J. Biol. Chem. 271, 19330-19337. DOI ScienceOn |
12 | Han, K., Kim, K. S., Bak, G., Park, H. and Lee, Y. (2010) Recognition and discrimination of target mRNAs by Sib RNAs, a cis-encoded sRNA family. Nucleic Acids Res. 38, 5851-5866. DOI ScienceOn |
13 | Singer, M. F., Jones, O. W. and Nirenberg, M. W. (1963) The effect of secondary structure of the template activity of polyribonucleotides. Proc. Natl. Acad. Sci. U. S. A. 49, 392-399. DOI ScienceOn |
14 | Paterson, B. M., Roberts, B. E. and Kuff, E. L. (1977) Structural gene identification and mapping by DNA-mRNA hybrid-arrested cell-free translation. Proc. Natl. Acad. Sci. U. S. A. 74, 4370-4374. DOI ScienceOn |
15 | Good, L., Awasthi, S. K., Dryselius, R., Larsson, O. and Nielsen, P. E. (2001) Bactericidal antisense effects of peptide-PNA conjugates. Nat. Biotechnol. 19, 360-364. DOI ScienceOn |
16 | De Lay, N., Schu, D. J. and Gottesman, S. (2013) Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices. J. Biol. Chem. 288, 7996-8003. DOI ScienceOn |
17 | Rasmussen, A. A., Johansen, J., Nielsen, J. S., Overgaard, M., Kallipolitis, B. and Valentin-Hansen, P. (2009) A conserved small RNA promotes silencing of the outer membrane protein YbfM. Mol. Microbiol. 72, 566-577. DOI ScienceOn |
18 | Urban, J. H. and Vogel, J. (2007) Translational control and target recognition by Escherichia coli small RNAs in vivo. Nucleic Acids Res. 35, 1018-1037. DOI ScienceOn |
19 | Gottesman, S. and Storz, G. (2011) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb. Perspect Biol. 3, a003798. |
20 | Chae, H., Han, K., Kim, K. S., Park, H., Lee, J. and Lee, Y. (2011) Rho-dependent termination of ssrS (6S RNA) transcription in Escherichia coli: implication for 3' processing of 6S RNA and expression of downstream ygfA (putative 5-formyl-tetrahydrofolate cyclo-ligase). J. Biol. Chem. 286, 114-122. DOI ScienceOn |
21 | Lee, J. Y., Park, H., Bak, G., Kim, K. S. and Lee, Y. (2013) Regulation of transcription from two ssrS promoters in 6S RNA biogenesis. Mol. Cells 36, 227-234. DOI |
22 | Kim, D. H., Behlke, M. A., Rose, S. D., Chang, M. S., Choi, S. and Rossi, J. J. (2005) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat. Biotechnol. 23, 222-226. DOI ScienceOn |
23 | Park, H., Bak, G., Kim, S. C. and Lee, Y. (2013) Exploring sRNA-mediated gene silencing mechanisms using artificial small RNAs derived from a natural RNA scaffold in Escherichia coli. Nucleic Acids Res. 41, 3787-3804. DOI ScienceOn |
24 | Murakawa, G. J. and Nierlich, D. P. (1989) Mapping the lacZ ribosome binding site by RNA footprinting. Biochemistry 28, 8067-8072. DOI |
25 | Morita, T. and Aiba, H. (2011) RNase E action at a distance: degradation of target mRNAs mediated by an Hfq-binding small RNA in bacteria. Genes Dev. 25, 294-298. DOI ScienceOn |
26 | Frohlich, K. S. and Vogel, J. (2009) Activation of gene expression by small RNA. Curr. Opin. Microbiol. 12, 674-682. DOI ScienceOn |
27 | Nakashima, N., Tamura, T. and Good, L. (2006) Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli. Nucleic Acids Res. 34, e138. DOI ScienceOn |
28 | Opdyke, J. A., Kang, J. G. and Storz, G. (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J. Bacteriol. 186, 6698-6705. DOI ScienceOn |
29 | Georg, J. and Hess, W. R. (2011) cis-antisense RNA, another level of gene regulation in bacteria. Microbiol. Mol. Biol. Rev. 75, 286-300. DOI ScienceOn |
30 | Opdyke, J. A., Fozo, E. M., Hemm, M. R. and Storz, G. (2011) RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J. Mol. Biol. 406, 29-43. DOI ScienceOn |
31 | Thakur, N., Qureshi, A. and Kumar, M. (2011) VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res. 40, D230-D236. |
32 | Matveeva, O., Nechipurenko, Y., Rossi, L., Moore, B., Saetrom, P., Ogurtsov, A. Y., Atkins, J. F. and Shabalina, S. A. (2007) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res. 35, e63. DOI |
33 | Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. S. and Khvorova, A. (2004) Rational siRNA design for RNA interference. Nat. Biotechnol. 22, 326-330. DOI ScienceOn |
34 | Calvori, C., Frontali, L., Leoni, L. and Tecce, G. (1965) Effect of rifamycin on protein synthesis. Nature 207, 417-418. DOI ScienceOn |
35 | Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415. DOI ScienceOn |
36 | Zhang, X. and Bremer, H. (1995) Control of the Escherichia coli rrnB P1 promoter strength by ppGpp. J. Biol. Chem. 270, 11181-11189. DOI ScienceOn |
37 | Pedersen, S. and Reeh, S. (1978) Functional mRNA half lives in E. coli. Mol. Gen. Genet. 166, 329-336. |
38 | Thomason, M. K., Fontaine, F., De Lay, N. and Storz, G. (2012) A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol. Microbiol. 84, 17-35. DOI ScienceOn |
39 | Yuan, B., Latek, R., Hossbach, M., Tuschl, T. and Lewitter, F. (2004) siRNA Selection Server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res. 32, W130-134. DOI ScienceOn |