Browse > Article
http://dx.doi.org/10.5483/BMBRep.2014.47.10.281

Secondary structure of the Irf7 5'-UTR, analyzed using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension)  

Kim, Yun-Mi (Department of Integrated OMICs for Biomedical Science, Yonsei University)
Choi, Won-Young (Department of Biochemistry, Yonsei University)
Oh, Chang-Mok (Department of Biotechnology, Yonsei University)
Han, Gyoon-Hee (Department of Integrated OMICs for Biomedical Science, Yonsei University)
Kim, Young-Joon (Department of Integrated OMICs for Biomedical Science, Yonsei University)
Publication Information
BMB Reports / v.47, no.10, 2014 , pp. 558-562 More about this Journal
Abstract
OASL1 is a member of the 2'-5'-oligoadenylate synthetase (OAS) family and promotes viral clearance by activating RNase L. OASL1 interacts with the 5'-untranslated region (UTR) of interferon regulatory factor 7 (Irf7) and inhibits its translation. To identify the secondary structure required for OASL1 binding, we examined the 5'-UTR of the Irf7 transcript using "selective 2'-hydroxyl acylation analyzed by primer extension" (SHAPE). SHAPE takes advantage of the selective acylation of residues in single-stranded regions by 1-methyl-7-nitroisatoic anhydride (1M7). We found five major acylation sites located in, or next to, predicted single-stranded regions of the Irf7 5'-UTR. These results demonstrate the involvement of the stem structure of the Irf7 5'-UTR in the regulation of Irf7 translation, mediated by OASL1.
Keywords
Irf7; OASL1; SHAPE; Secondary structure; 1M7;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Lee, M. S., Kim, B., Oh, G. T. and Kim, Y. J. (2013) OASL1 inhibits translation of the type I interferon-regulating transcription factor Irf7. Nat. Immunol. 14, 346-355.   DOI   ScienceOn
2 Taniguchi, T., Ogasawara, K., Takaoka, A. and Tanaka, N. (2001) IRF family of transcription factors as regulators of host defense. Annu. Rev. Immunol. 19, 623-655.   DOI   ScienceOn
3 Takaoka, A., Tamura, T. and Taniguchi, T. (2008) Interferon regulatory factor family of transcription factors and regulation of oncogenesis. Cancer Sci. 99, 467-478.   DOI   ScienceOn
4 Honda, K., Yanai, H., Negishi, H., Asagiri, M., Sato, M., Mizutani, T., Shimada, N., Ohba, Y., Takaoka, A., Yoshida, N. and Taniguchi, T. (2005) IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434, 772-777.   DOI   ScienceOn
5 Ning, S., Pagano, J. S. and Barber, G. N. (2011) Irf7: activation, regulation, modification and function. Genes Immun. 12, 399-414.   DOI   ScienceOn
6 Sato, M., Hata, N., Asagiri, M., Nakaya, T., Taniguchi, T. and Tanaka, N. (1998) Positive feedback regulation of type I IFN genes by the IFN-inducible transcription factor IRF-7. FEBS Lett. 441, 106-110.   DOI   ScienceOn
7 Akira, S., Uematsu, S. and Takeuchi, O. (2006) Pathogen recognition and innate immunity. Cell 124, 783-801.   DOI   ScienceOn
8 Lee, M. S. and Kim, Y. J. (2007) Signaling pathways downstream of pattern-recognition receptors and their cross talk. Annu. Rev. Biochem. 76, 447-480.   DOI   ScienceOn
9 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.   DOI   ScienceOn
10 Wan, Y., Qu, K., Ouyang, Z. and Chang, H. Y. (2013) Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat. Protoc. 8, 849-869.   DOI   ScienceOn
11 Low, J. T. and Weeks, K. M. (2010) SHAPE-directed RNA secondary structure prediction. Methods 52, 150-158.   DOI   ScienceOn
12 Mortimer, S. A. and Weeks, K. M. (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc. 129, 4144-4145.   DOI   ScienceOn
13 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.   DOI   ScienceOn
14 Wang, Z., Parisien, M., Scheets, K. and Miller, W. A. (2011) The cap-binding translation initiation factor, eIF4E, binds a pseudoknot in a viral cap-independent translation element. Structure 19, 868-880.   DOI   ScienceOn
15 Bevilacqua, A., Ceriani, M. C., Capaccioli, S. and Nicolin, A. (2003) Post-transcriptional regulation of gene expression by degradation of messenger RNAs. J. Cell. Physiol. 195, 356-372.   DOI   ScienceOn
16 Turner, R., Shefer, K. and Ares, M., Jr. (2013) Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7). RNA 19, 1857-1863.   DOI   ScienceOn
17 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.   DOI   ScienceOn
18 Deigan, K. E., Li, T. W., Mathews, D. H. and Weeks, K. M. (2009) Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. U. S. A. 106, 97-102.   DOI   ScienceOn
19 Gherghe, C. M., Shajani, Z., Wilkinson, K. A., Varani, G. and Weeks, K. M. (2008) Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J. Am. Chem. Soc. 130, 12244-12245.   DOI   ScienceOn
20 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.   DOI   ScienceOn
21 Tijerina, P., Mohr, S. and Russell, R. (2007) DMS footprinting of structured RNAs and RNA-protein complexes. Nat. Protoc. 2, 2608-2623.   DOI   ScienceOn