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<p>Short linear motifs (SLiMs) are the most ubiquitous protein interaction motifs within unstructured regions of the human proteome, yet their contribution to cellular homeostasis remains poorly understood. Here, 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 reported 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 many predicted SLiMs affecting proliferation do not belong to existing classes and identify binding partners for several of these, providing mechanistic insight into a disease-associated <i>ANKRD17</i> mutation. Our study provides a proteome-wide resource on SLiM essentiality uncovering numerous uncharacterized essential SLiMs.</p>

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A proteome-wide dependency map of protein interaction motifs

  • 期刊论文

  • 发表日期：

    2026年3月6日

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  • Sara M. Ambjørn,
  • Bob Meeusen,
  • Johanna Kliche,
  • Juanjuan Wang,
  • Dimitriya H. Garvanska,
  • Thomas Kruse,
  • Blanca Lopez Mendez,
  • Matthias Mann,
  • Niels Mailand,
  • Emil P. T. Hertz,
  • Norman E. Davey,
  • Jakob Nilsson

摘要

Short linear motifs (SLiMs) are the most ubiquitous protein interaction motifs within unstructured regions of the human proteome, yet their contribution to cellular homeostasis remains poorly understood. Here, 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 reported 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 many predicted SLiMs affecting proliferation do not belong to existing 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 uncovering numerous uncharacterized essential SLiMs.