19 Cellular Internal Ribosome Entry Site Elements and the Use of cDNA Microarrays in Their Investigation

The discovery that picornaviral RNA genomes are translated by an internal ribosome entry mechanism (see Chapter 4) raised the question whether host cell mRNAs could use this initiation mechanism as well. This idea was supported by the finding that internal initiation could operate on viral internal ribosome entry sites (IRES) both in cultured cells (Pelletier and Sonenberg 1988; Jang et al. 1989) and in cell-free systems (Jang et al. 1988; Pelletier and Sonenberg 1989) in the absence of any viral factors, suggesting that the eukaryotic translation apparatus can perform internal initiation. As discussed in Chapter 4, IRES elements can promote translation in the absence of a functional 5′ cap-binding protein complex eIF4F, composed of factors eIF4E, eIF4A, and eIF4G. Thus, it was not too surprising when the first cellular IRES-containing mRNA, encoding the immunoglobulin binding protein BiP (Ting and Lee 1988), was identified by its ability to be translated in poliovirus-infected cells when overall translation of host cell mRNAs was inhibited as a result of eIF4G degradation (Sarnow 1989). Translation assays with dicistronic mRNAs that contained the 5′ noncoding region (5′NCR) of BiP inserted between two reporter cistrons revealed that the BiP 5′NCR could mediate translation of the second cistron without a requirement for ribosomes to traverse the first cistron (Macejak and Sarnow 1991). This result strongly suggested that the BiP 5′NCR functions as an IRES which can bind ribosomes directly and mediate translation of open reading frames, located downstream. The identification of further cellular mRNAs with IRES elements has...