Genome-wide pharmacological modulation of cap-dependent translational control

Abstract

The first step of cap-dependent translation is mediated by the mRNA cap-binding protein eukaryotic initiation factor 4E (eIF4E). Although involved in translating nearly all cellular transcripts, mRNAs vary widely in their translational response to eIF4E activity changes. Prior studies of mRNA structure revealed several features governing eIF4E responsiveness; however, most of this knowledge is based on comparison of two levels of eIF4E activity with unclear physiological relevance. To identify mRNA structural features that govern genome-wide ribosome recruitment across a full range of physiological eIF4E activities, we precisely modulated eIF4E activity using an eIF4E-inducible system together with 4Ei-1, an inhibitor of the eIF4E-5'mRNA cap association. We identified genes that were more (4E hypersensitive) or less (4E hyposensitive) responsive to eIF4E activity changes than average. Distinct characteristics associated with each class: 4E hypersensitive genes had longer 5'UTRs with higher GC content, longer 3'UTRs with lower GC content; more AU-rich elements and a higher density of unique microRNA targets sites than typical genes. Importantly, these structural characteristics predicted the translational response across the dose range of 4Ei-1. Gene ontology analysis showed an association between 4E hypersensitive genes and proliferation; and cell cycle experiments with 4Ei-1 validated this result. A search for the outcome and mechanism of this proliferative gene activation in a physiological setting revealed that abrupt gain of eIF4E function in quiescent cells first triggers G0 exit and then cell cycle transit at least partially by increasing ribosome recruitment to cyclins C and D1. Whereas cyclin C is not necessary for this effect; cyclin D1 is indispensable, although not sufficient. Our findings provide important insights into mRNA properties of eIF4E-modulated translational control.