Protein Depletion in Caenorhabditis elegans Using the Auxin-Inducible Degradation System

The auxin-inducible degradation (AID) system is a powerful tool in modern molecular genetics that allows for conditional protein depletion. In Caenorhabditis elegans, tools exist to allow for rapid, tissue-specific depletion of target proteins. The system requires tagging a gene of interest with an AID degron and a transgene expressing the Arabidopsis thaliana TIR1 F-box protein, which can form a functional SCF ubiquitin ligase with endogenous Skp and Cullin proteins. Here, I describe how to generate degron knock-ins by CRISPR, cross them to TIR1-expressing strains, and perform depletion experiments. I provide a description of our current methods and highlight alternative approaches.