Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control

The synthesis of proteins in multicellular organisms needs to be carefully tuned to changing proteome demands during development, and defects in this process often have a disproportionate impact in specific cell types and tissues. Here, we compared the essentiality of 262 genes from the mRNA translation machinery by inducible CRISPRi screens in HEK293 cells, human induced pluripotent stem cells (hiPSC) and hiPSC-derived neuronal progenitor cells, neurons, and cardiomyocytes. While ribosomal proteins and core translation factors were broadly essential, the cellular responses and phenotypic consequences of perturbing translation-dependent quality control pathways were highly dependent on the cellular context. By profiling ribosome occupancy in cells that are particularly sensitive to ZNF598 loss, we discovered a previously unappreciated role of this protein in detecting ribosome collisions during translation initiation. Our findings illuminate the importance of cell identity for deciphering the molecular mechanisms of translational control in metazoans. Overall design: Ribosome profiling libraries generated from human induced pluripotent stem cells depleted for ZNF598 by CRISPRi or expressing a ZNF598 RING domain mutant.