Nucleic Acids Research Advance Access originally published online on June 25, 2007
Nucleic Acids Research 2007 35(14):4664-4677; doi:10.1093/nar/gkm483
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Nucleic Acids Research, 2007, Vol. 35, No. 14 4664-4677
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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A search for structurally similar cellular internal ribosome entry sites
1Department of Biochemistry, Microbiology and Immunology, 2Department of Pediatrics and 3School of Information Technology and Engineering, University of Ottawa, ON, Canada and 4Apoptosis Research Centre, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada, K1H 8L1
*To whom correspondence should be addressed. Tel: +613 738 3207; Fax: +613 738 4833; Email: martin{at}arc.cheo.ca
Received May 15, 2007. Revised May 31, 2007. Accepted June 4, 2007.
Internal ribosome entry sites (IRES) allow ribosomes to be recruited to mRNA in a cap-independent manner. Some viruses that impair cap-dependent translation initiation utilize IRES to ensure that the viral RNA will efficiently compete for the translation machinery. IRES are also employed for the translation of a subset of cellular messages during conditions that inhibit cap-dependent translation initiation. IRES from viruses like Hepatitis C and Classical Swine Fever virus share a similar structure/function without sharing primary sequence similarity. Of the cellular IRES structures derived so far, none were shown to share an overall structural similarity. Therefore, we undertook a genome-wide search of human 5'UTRs (untranslated regions) with an empirically derived structure of the IRES from the key inhibitor of apoptosis, X-linked inhibitor of apoptosis protein (XIAP), to identify novel IRES that share structure/function similarity. Three of the top matches identified by this search that exhibit IRES activity are the 5'UTRs of Aquaporin 4, ELG1 and NF-kappaB repressing factor (NRF). The structures of AQP4 and ELG1 IRES have limited similarity to the XIAP IRES; however, they share trans-acting factors that bind the XIAP IRES. We therefore propose that cellular IRES are not defined by overall structure, as viral IRES, but are instead dependent upon short motifs and trans-acting factors for their function.
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