Abstract
The internal ribosome entry site (IRES) is a part of the mRNA
sequence which is able to attract the eukaryotic ribosomal initiation
complex and to directly promote the initiation of protein synthesis
independently of the presence of 5'-terminal 7mG cap. RNA structures
bearing the IRES activity were first discovered in certain eukaryotic
viruses where they very often play a pivotal role in viral strategies,
allowing the viral invader to overcome the overall decrease of the
host protein synthesis caused either by viral proteins or by the
cellular antiviral defense system. Although the IRES segments and thus
the cap-independent translation initiation were first described in
viruses, extensive evidence has appeared in the past few years that a
similar principle of the translation initiation is utilized also by
some cellular mRNAs. Demonstration of IRES activity of a particular
RNA region is not a simple task. A proper design of the experiment
and a careful selection of the controls - excluding artificial signals
generated by leaky scanning, ribosome hopping and undesirable cryptic
transcription, splicing or physical breakage at the hot-spots - are
very important. A number of false positives described in the
literature as well as difficulties in designing appropriate controls
have become the major stimuli for creating IRESite - the publicly
available manually annotated database of experimentally verified IRES
structures. This chapter presents the current status of the IRESite
database (http://www.iresite.org), the complete list of known viral
and cellular IRESs as well as novel results obtained from the
comparative analyses of IRES segments accumulated to date. The article
also presents a brief description and comparison of other available
databases containing IRES and 5' untranslated region (5'-UTR) related
information.
*Corresponding authors: M. Mokrejš <mmokrejs --at-- iresite.org>, M. Pospíšek <martin --at-- natur.cuni.cz>
Full citation
Mokrejs M., Vopalensky V., Masek T., Pospisek M. (2007) Title: A Bioinformatical Approach to the Analysis of Viral and Cellular Internal Ribosome Entry Sites. In: Columbus F editors. New Messenger RNA Research Communications. Hauppauge, NY: Nova Science Publishers; pp. 133-166.