Figure 1. mTOR Inhibition Depletes mRNAs with Functions in AA Transport and Metabolism.
(A) Global changes in mRNA levels following 24 hr of mTOR inhibition. HEK293T cells were treated with vehicle (DMSO) or 250 nM Torin 1 for 24 hr and analyzed by RNA-seq.
(B) mTOR inhibition reduces mRNAs with functions in AA metabolism and transport. Gene set enrichment analysis (GSEA) was used to analyze changes in mRNA levels from (A). Vertical lines beneath the x axis denote the members of each gene set. (AA Metabolic process, MSIGDB M11769; AA/Oligopeptide SLC Transporters, MSIGDB 19056; tRNA Aminoacylation, MSIGDB M456).
(C) Left panel: an mTOR-regulated gene module. CCLE expression data were clustered by Pearson correlation and shown as a heatmap (increases in red and decreases in blue). Middle panel: log2-fold changes in mRNA levels from (A) were summed in a 25-gene window and plotted at each position. Right panel: a zoomed-in view of the cluster indicated is shown. mRNAs repressed upon mTOR inhibition are highlighted in red.
(D) ATF4-binding motif from the JASPAR database of transcription factor-binding sites, identified by motif analysis of promoters of genes in (C) (see the Supplemental Experimental Procedures).
(E) Extracts from cells treated as in (A) were analyzed for the indicated proteins by immunoblotting.