Extended Data Fig. 7: Translational reprogramming by bi-steric and active-site inhibitors of mTOR is modulated by inhibition of mTORC1.

a, Scatter plots of polysome-associated RNA vs. cytosolic RNA log2 fold changes for the four comparisons: DMSO (complete media) vs. starvation [top left], MLN0128 vs. DMSO [top right], BiS-13x vs. MLN0128 [bottom left] and BiS-35x vs. MLN0128 [bottom right]. For each comparison, genes are colored according to their mode for regulation of gene expression derived from analysis using anota2seq⁵⁰ and the number of such regulated transcripts is indicated: ‘translation’ denotes transcripts whose change in polysome-association (up or down) could not be explained by a corresponding change in total mRNA level (that is changes in translational efficiency leading to altered protein level); ‘buffering’ denotes transcripts whose change in the total mRNA pool (up or down) was offset at the level of translation such that the association with polysomes remained largely unaltered (that is a change in total mRNA level opposed by a change in translational efficiency, which is expected to lead to unaltered protein levels despite changes in mRNA levels [as recently described]^55,56; ‘abundance’ denotes transcript which show a similar change in the total mRNA pool and association with polysomes (that is a change in transcription or mRNA stability leading to altered protein level). b, Samples from the polysome-profiling experiment (normalized data) were projected on the 2 first components of a centered principal component analysis (the proportion of the variance explained by each component is indicated). Data points are colored according to their RNA source (total mRNA or polysome-associated mRNA), shapes denote treatments (DMSO, MLN0128, BiS-13, BiS-35x, or starvation) and the numbers indicate biological replicates (1-4). The library preparation was performed twice on biological replicate 1 providing 2 technical replicates labeled 1 A and 1B. Replicate 1 A was excluded from the downstream analysis.