A proteome-wide dependency map of protein interaction motifs

Abstract

Short linear motifs (SLiMs) are the most ubiquitous protein interaction modules within unstructured regions of the human proteome, yet their contribution to cellular homeostasis remains poorly understood. To systematically assess SLiM function, we applied base editing to mutate all reported and a set of computationally predicted SLiMs defined by SLiM-like evolutionary patterns. By screening 7,293 SLiM-containing regions with 80,473 mutations in HAP1 cells, we define a SLiM dependency map identifying 450 known and 264 predicted SLiMs required for normal cell proliferation. Mutational consequences were highly reproducible in RPE1 cells, with differences attributed to cell line-specific gene essentiality. We show that most essential predicted SLiMs belong to novel classes and identify binding partners for several of these, providing mechanistic insight into a disease-associated ANKRD17 mutation. Our study provides a proteome-wide resource on SLiM essentiality and uncovers numerous uncharacterized yet essential SLiMs.