mTORC1 hyperactivation blocks pluripotent stem cells fate transitions through TFE3-NuRD association

As an evolutionarily conserved master regulator of metabolism, mechanistic target of rapamycin complex 1 (mTORC1) regulates cell states and fates in development, cancer and aging. mTORC1 activity regulation was critical for pluripotent stem cells maintenance and cell fate transitions. Inhibition of mTORC1 induces embryonic stem cells (ESCs) entry into a paused state which reversibly arrests self-renewal leaving pluripotency intact. Hyperactivation of mTORC1 impedes both pluripotency re-establishment and exit of PSCs. As shown that mTORC1 mediates TFE3 nuclear translocation block pluripotency exit, whether similar mechanisms through transcription factor TFE3 are involved in these processes, and the detailed mechanism by which mTORC1-TFE3 regulates critical transcriptional processes for these transitions, remain unclear. In this study, we demonstrate that the nuclear translocation of TFE3, induced by hyperactivation of mTORC1, results in its binding to the nucleosome remodeling and deacetylation (NuRD) complex in both re-establishment and exit of pluripotency. This interaction inhibits the expression of various crucial genes during different fate transitions of PSCs. Our findings uncover a common and key role of TFE3-NuRD association as mediator of mTORC1 to block pluripotent cell fate transitions, with implications for various fields including physiological and pathological diseases. This submission contains two parts, The first part includes CUT&TAG profiles of TFE3 and RBBP4 in OSKM-induced reprogramming (D12) iPSCs under three conditions: wild-type (WT), Tsc1 knockout (KO), and Tsc1 KO with Rapamycin (0.3nM) treatment; and the second part CUT&Tag sequencing data from mouse embryonic stem cells (mESCs) under different culture conditions and genetic backgrounds. The dataset includes eight samples representing: (1) wild-type , (2) Tsc1 knockout (Tsc1 KO), and (3) Tsc1 KO with rapamycin treatment (0.3nM) mESCs cultured in either 2iL (pluripotency-maintaining) or N2B27 (differentiation, 40h) conditions. For each sample group, chromatin profiling was performed using antibodies targeting the transcription factor TFE3 and the NuRD complex subunit RBBP4.