Genetically targeted mTORC1 inhibitor reveals transcriptional control by nuclear mTORC1

mTORC1 is a nutrient sensor which integrates diverse inputs to regulate protein translation and cell growth. While mTORC1 is activated on the lysosome in the classical model, it has become increasingly clear that this multifaceted signaling complex is active at various subcellular locations, such as the nucleus. However, what specific functions mTORC1 serves at these locations and how its signaling is compartmentalized are not unclear. To interrogate subcellular pools of mTORC1, we developed TerminaTOR, a genetically encodable inhibitor of mTORC1 that can be targeted to specific subcellular locations. When TerminaTOR is directed to the lysosome, it inhibits canonical lysosomal mTORC1 and induces autophagy. Furthermore, TerminaTOR targeted to the nucleus specifically inhibits nuclear mTORC1, uncovering non-canonical roles of nuclear mTORC1 in regulating the transcription of CCAAT motif-containing genes. Thus, mTORC1 exhibits functional spatial compartmentalization, and TerminaTOR serves as a powerful tool for unraveling spatially regulated functions of mTORC1 across different scales Overall design: We generated two doxycycline inducible stably NIH3T3 cell lines that express H2A-mCherry (Control) or H2A-TerminaTOR (Nuclear TerminaTOR), which specifically inhibits nuclear mTORC1 activity. We then starved and stimulated the cells with PDGF to induce nuclear mTORC1 activity. We collected RNA samples and conducted RNA-seq to understand the nuclear mTORC1-controlled transcription.