nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs

Abstract

The diversity of MTOR-regulated mRNA translation remains unresolved. Whereas ribosome-profiling suggested that MTOR almost exclusively stimulates translation of the TOP (terminal oligopyrimidine motif) and TOP-like mRNAs, polysome-profiling indicated that MTOR also modulates translation of mRNAs without the 5′ TOP motif (non-TOP mRNAs). We demonstrate that in ribosome-profiling studies, detection of MTOR-dependent changes in non-TOP mRNA translation was obscured by low sensitivity and methodology biases. Transcription start site profiling using nano-cap analysis of gene expression (nanoCAGE) revealed that not only do many MTOR-sensitive mRNAs lack the 5′ TOP motif but that 5′ UTR features distinguish two functionally and translationally distinct subsets of MTOR-sensitive mRNAs: (1) mRNAs with short 5′ UTRs enriched for mitochondrial functions, which require EIF4E but are less EIF4A1-sensitive; and (2) long 5′ UTR mRNAs encoding proliferation- and survival-promoting proteins, which are both EIF4E- and EIF4A1-sensitive. Selective inhibition of translation of mRNAs harboring long 5′ UTRs via EIF4A1 suppression leads to sustained expression of proteins involved in respiration but concomitant loss of those protecting mitochondrial structural integrity, resulting in apoptosis. Conversely, simultaneous suppression of translation of both long and short 5′ UTR mRNAs by MTOR inhibitors results in metabolic dormancy and a predominantly cytostatic effect. Thus, 5′ UTR features define different modes of MTOR-sensitive translation of functionally distinct subsets of mRNAs, which may explain the diverse impact of MTOR and EIF4A inhibitors on neoplastic cells.

Prosapip1-Dependent Synaptic Adaptations in the Nucleus Accumbens Drive Alcohol Intake, Seeking, and Reward

“…Curiously, however, out of the 12 identified transcripts, only RasGRP4 mRNA sequence contains a TOP-like motif (data not shown). However, recent studies suggest that the regulation of mRNA translation by mTORC1 signaling is not limited to TOP and TOP-like sequences (Gandin et al, 2016; Morita et al, 2013). Interestingly, three candidates are related to the microRNA (miRNA) gene-silencing machinery.…”

Translational control by 5′-untranslated regions of eukaryotic mRNAs

“…mTOR complex 1 (mTORC1) activates the La-related protein 1 (LARP1) that binds to the TOP sequence (52). Many lessabundant mRNAs lacking 5′TOP exhibit mTOR dependence, encoding mitochondrial and growth/ survival-promoting proteins (53). Additionally, the m 6 -adenine methylation of 5′UTR sequences seems to have stimulatory effects (54).…”

IL-15 activates mTOR and primes stress-activated gene expression leading to prolonged antitumor capacity of NK cells

“…Moreover, each regulatory mode targeted a specific set of functions: cytokine-primed upregulated genes were enriched for functions related to respiration, metabolic processes, and translation; cytokine-primed downregulated genes were enriched for transcription, cell signaling, and developmental processes; cytokine-induced upregulated genes were enriched for cell cycle functions; and cytokine-induced downregulated genes were BLOOD Our finding that cytokine-primed upregulated genes are enriched for regulation via differential translation and mitochondria-related functions parallels recent data on translational control of mitochondrial function via selective translation of mRNAs encoding mitochondria-related proteins downstream of the mTOR pathway. 25,26 Thus, it is plausible that differential activation of mTOR signaling by IL-2 or IL-15 could, at least partly, explain observed gene expression differences and associated cellular phenotypes. 25,27 Consistently, IL-15 induced increased phosphorylation of the mTOR substrate S6K, as compared with IL-2 and IL-15, associated S6K phosphorylation was maintained, albeit at a lower level, after 24 hours of cytokine withdrawal ( Figure 3C).…”