A landscape of functional lysine residues in cell fitness

Current CRISPR screens could effectively identify functional genes; however, more explicit genetic elements, such as codons of amino acids, still await a thorough interrogation. Here, we established a CRISPR platform for unbiasedly probing functional amino acid residues at the genome scale. By coupling adenine base editors and barcoded sgRNAs, we targeted 48% of the lysine codons in the coding genome and identified ~ 500 lysine codons whose mutations perturb cell proliferation, and some of those are implicated in cancer. These codons were then interpreted at the gene level by combining them with CRISPR knockout data, resulting in a functional landscape of lysine residues in cell fitness. Mining these data, we discovered that functional lysine residues are enriched in a CUL3-centric regulatory network. Mechanistic studies revealed lysine 171 of KCTD10, a substrate adaptor of CUL3, modulates cell fitness by recruiting mitotic proteins for degradation. Our research established a high-resolution functional genomics approach and provided valuable resources for understanding cell fitness regulation better.