Historically, the ribosome has been viewed as a ribozyme with constitutive rather than regulatory capacity in mRNA translation. However, emerging studies reveal that ribosome activity may be highly regulated to impart a new layer of specificity in control of gene expression and organismal biology. Heterogeneity in the composition of the ribosome may generate variations to the translation machinery that significantly impact on how the genomic template is translated into functional proteins.

Studies in our laboratory have shown that ribosomal protein RPL38 confers specificity to the ribosome and is responsible for specifically translating a subset of Homeobox (Hox) mRNAs to regulate the mammalian body plan. In Rpl38 mutant embryos, global protein synthesis is unchanged while the translation of 8 of the 39 Hox mRNAs is specifically affected. Unexpectedly, Rpl38 transcripts are highly enriched in a tissue specific manner, most notably in somites and within the neural tube. Together, these studies led us to propose that ribosome in distinct regions of the embryo may be highly specialized to exert transcript-specific translational control. However how transcripts are recognized and selected by RPL38 remains unknown.

Here I uncover a unique set of RNA regulons embedded in the 5'UTRs of Hox genes which are critical for ribosome-directed control of their spatiotemporal expression patterns. These structured RNA elements, resembling Viral Internal Ribosome Entry Sites (IRES), are positioned close to the AUG of subsets of Hox mRNA to interact with ribosomal proteins and directly recruit the ribosome. Using Hoxa9 as a model, I find that the IRES element folds into a stable structure in vitro and can recruit ribosomes directly to the mRNA. By generating the first targeted knock-out of an IRES element in the mouse, I show that the Hoxa9 transcript, despite numerous layers of transcriptional control, requires an IRES-element for accurate spatiotemporal expression and axial skeletal patterning. The unexpected requirement for specialized translation control of Hox transcripts is further explained by the activity of a novel Translational Inhibitory Element (TIE), which inhibits general cap-dependent translation, thereby converting a generic mode of mRNA translation into a highly specialized one. Together, these studies uncover a new paradigm of specialized translational regulation that is achieved through a combination of unique RNA regulons to facilitate ribosome-mediate control of gene expression.