%0 Journal Article %A Michael A. Martinez %A Brian A. Kinney %A Guinevere Ashley %A James M. Ragle %A Christopher M. Hammell %A Jordan D. Ward %A David Q. Matus %T A water-soluble, synthetic auxin analog for rapid degradation of target proteins during C. elegans development %D 2019 %R 10.1101/716837 %J bioRxiv %P 716837 %X As developmental biologists in the age of genome editing, we now have access to an ever-increasing array of tools to manipulate endogenous gene expression. By combining CRISPR/Cas9-genome engineering with heterologous systems for targeted protein degradation, researchers can gain the spatial and temporal control to dissect endogenous protein function during development. A recent addition to this toolkit is the auxin-inducible degradation system, which functions through the activity of a hormone-inducible Arabidopsis F-box protein, transport inhibitor response 1 (TIR1). In the presence of auxin, TIR1 serves as a substrate recognition component of the E3 ubiquitin ligase complex SKP1-CUL1-F-box (SCF), ubiquitinating auxin-inducible degron (AID)-tagged proteins for proteasomal degradation. This system has been used successfully in C. elegans, Drosophila, zebrafish, yeast, and mammalian cell culture for rapid targeted protein depletion. Here, we describe an improved protocol for the AID system in C. elegans, utilizing a cost-effective alternative to the natural auxin indole-3-acetic acid (IAA), 1-naphthaleneacetic acid (NAA). We take advantage of the increased water solubility of NAA and demonstrate through quantitative high-resolution spinning disk confocal microscopy that we can rapidly degrade target proteins within 30 minutes of NAA exposure. Additionally, we find that NAA works robustly in both growth media and aqueous buffer, allowing for comparative use among growth plates, liquid submersion and microfluidic devices. We provide evidence that TIR1 interacts with C. elegans CUL1 homolog, cul-1, to degrade target proteins. Finally, as a proof-of-principle, we demonstrate high-throughput, penetrant defects from AID-mediated depletion of the Ftz-F1 nuclear hormone receptor, nhr-25, during C. elegans uterine-vulval development, where early depletion of nhr-25 results in a failure to specify the uterine anchor cell and later depletion arrests the division of the vulval precursor cells that give rise to the adult egg-laying apparatus. Together, this work provides a streamlined protocol broadly applicable to targeted protein degradation methods for dissecting gene function throughout C. elegans development and homeostasis. %U https://www.biorxiv.org/content/biorxiv/early/2019/07/28/716837.full.pdf