Metabolic co-essentiality mapping identifies c12orf49 as a regulator of SREBP processing and cholesterol metabolism

Co-essentiality mapping has been useful to systematically cluster genes into biological pathways and identify gene functions1(–)3. Here, using the debiased sparse partial correlation (DSPC) method3, we construct a functional co-essentiality map for cellular metabolic processes across human cancer cell lines. This analysis reveals 35 modules associated with known metabolic pathways and further assigns metabolic functions to unknown genes. In particular, we discover C12orf49 as an essential regulator of cholesterol and fatty acid metabolism in mammalian cells. Mechanistically, C12orf49 localizes to the Golgi, binds site 1 protease (MBTPS1) and is necessary for the cleavage of its substrates, including SREBP transcription factors. This function depends on the evolutionarily conserved uncharacterized domain (DUF2054) and promotes cell proliferation under cholesterol depletion. Notably, c12orf49 depletion in zebrafish blocks dietary lipid clearance in vivo, phenocopying mbtps1 mutants. Finally, in an EHR-linked DNA biobank, C12orf49 is associated with hyperlipidemia through phenome analysis. Altogether, our findings reveal a conserved role for C12orf49 in cholesterol and lipid homeostasis and provide a platform to identify unknown components of other metabolic pathways.