Pooled CRISPR/Cas9 screen for genes that contribute to ribosome biogenesis and turnover

While features of ribosome assembly are shared between species, our understanding of the diversity, complexity, dynamics, and regulation of ribosome production in multicellular organisms remains incomplete. To gain insights into ribosome biogenesis in human cells, we performed a genome wide loss of function screen combined with differential labeling of pre-existing and newly assembled ribosomes. These efforts identified two functionally uncharacterized genes, C1ORF09 and SPATA5. We provide evidence that these factors, together with CINP and SPATA5L1, control a late step of human pre-60S maturation in the cytoplasm. Loss of either C1ORF109 or SPATA5 impairs global protein synthesis. These results link ribosome assembly with neurodevelopmental disorders associated with recessive SPATA5 mutations. Based on these findings, we propose the expanded repertoire of ribosome biogenesis factors likely enables multicellular organisms to coordinate multiple steps of ribosome production in response to different developmental and environmental stimuli. Overall design: A genome-scale CRISPR/Cas9-mediated loss of function screen for ribosome biogenesis/turnover factors was performed in HEK293T cells with endogenous RPL28-SNAP tagging. The pre-existing and newly produced ribosomes were differentially labeled with red and green fluorescence for FACS enrichment.