Modulation of nonsense mediated decay by rapamycin

Abstract

Rapamycin is a naturally occurring macrolide whose target is at the core of nutrient and stress regulation in a wide range of species. Despite well-established roles as an inhibitor of cap-dependent mRNA translation, relatively little is known about its effects on other modes of RNA processing. Here, we characterize the landscape of rapamycin-induced post-transcriptional gene regulation. Transcriptome analysis of rapamycin-treated cells reveals genome-wide changes in alternative mRNA splicing and pronounced changes in NMD-sensitive isoforms. We demonstrate that despite well-documented attenuation of cap-dependent mRNA translation, rapamycin can augment NMD of certain transcripts. Rapamycin-treatment significantly reduces the levels of both endogenous and exogenous Premature Termination Codon (PTC)-containing mRNA isoforms and its effects are dose-, UPF1- and 4EBP-dependent. The PTC-containing SRSF6 transcript exhibits a shorter half-life upon rapamycin-treatment as compared to the non-PTC isoform. Rapamycin-treatment also causes depletion of PTC-containing mRNA isoforms from polyribosomes, underscoring the functional relationship between translation and NMD. Enhanced NMD activity also correlates with an enrichment of the nuclear Cap Binding Complex (CBC) in rapamycin-treated cells. Our data demonstrate that rapamycin modulates global RNA homeostasis by NMD.

Dietary restriction induces posttranscriptional regulation of longevity genes

“…Our analysis of intron retention suggested that coupling of AS-NMD is modulated under DR, in part, by changing the selectivity toward which transcripts are detected and degraded. Observations are in line with those obtained from cell culture exposed to rapamycin, a drug that inhibits the DR-related TOR pathway, in which the selectivity of NMD toward transcripts was also modulated (Martinez-Nunez et al, 2016). Taken together, studies point to an adaptive mechanism of DR that functions by controlling productive splicing and turnover.…”

Dietary restriction induces post-transcriptional regulation of longevity genes

“…Our analysis of intron retention suggested that coupling of AS-NMD is modulated under DR, in part, by changing the selectivity towards which transcripts are detected and degraded. Observations are in line with those obtained from cell culture exposed to rapamycin, a drug that inhibits the DR-related TOR pathway, in which the selectivity of NMD towards transcripts was also modulated (Martinez-Nunez et al, 2016). Taken together, studies point to an adaptive mechanism of DR that functions by controlling productive splicing and turnover.…”

Identifying the Translatome of Mouse NEBD-Stage Oocytes via SSP-Profiling; A Novel Polysome Fractionation Method

“…For almost 50 years, polysome profiling has provided a gold-standard method to precisely assay functional genome readout at a given time point [5]. Indeed, it has for many years been widely applied to assess translational fitness under various physiological conditions relating to cellular stress [6][7][8][9], as well as being applied to study ribosome biogenesis and the functional roles of proteins involved in translation, regulation of mRNA stability and miRNA-mediated silencing [10][11][12][13]. Although, originally established in yeast, polysome profiling has been successfully introduced in mammalian cell, plant, bacteria and translation competent cell-free model systems [14][15][16][17].…”