In RNAi (RNA interference), siRNAs (small interfering RNAs) are loaded into the RISC (RNA-induced silencing complex), which then mediates endonucleolytic cleavage of complementary target RNAs. Although RNAi has become one of the most powerful tools in molecular biology to assess gene function, there remains a great number of ineffective siRNAs. It is already known that the assembly and activation of RISC is a crucial determinant of RNAi activity, but downstream effects such as target accessibility have not been analysed extensively. Therefore we assessed the effect of target site accessibility and found that it significantly improves the potency of siRNAs. Similarly, miRNAs (microRNAs) act by repressing protein synthesis through imperfect base-pairing to the 3′-UTR (untranslated region) of target mRNAs. We found that predicted target sites reside in regions of high accessibility and tested whether this criterion could be used in the search of functional miRNA targets. In addition, we performed reporter gene assays to test whether accessibility correlates with measured mRNA suppression levels. The results of our initial study suggest that secondary structures might add a so far underrepresented layer of complexity in the recognition of RNA targets by miRNAs.
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December 2008
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Conference Article|
November 19 2008
Target site effects in the RNA interference and microRNA pathways
Gregor Obernosterer;
Gregor Obernosterer
1
*Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
1To whom correspondence should be addressed (email gregor.obernosterer@imba.oeaw.ac.at).
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Hakim Tafer;
Hakim Tafer
†Institute of Theoretical Biochemistry (TBI), University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
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Javier Martinez
Javier Martinez
*Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Publisher: Portland Press Ltd
Received:
July 04 2008
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© The Authors Journal compilation © 2008 Biochemical Society
2008
Biochem Soc Trans (2008) 36 (6): 1216–1219.
Article history
Received:
July 04 2008
Citation
Gregor Obernosterer, Hakim Tafer, Javier Martinez; Target site effects in the RNA interference and microRNA pathways. Biochem Soc Trans 1 December 2008; 36 (6): 1216–1219. doi: https://doi.org/10.1042/BST0361216
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