TAG-IN, a swappable strategy for endogenous gene tagging in <i>Caenorhabditis elegans</i> using cassette exchange

Endogenous gene tagging allows researchers to study genes in their native genomic context, underscoring the need for efficient and scalable tagging approaches. Here, we report TAG-IN, a streamlined and swappable strategy for tagging virtually any gene in the <i>C. elegans</i> genome. A seed allele for the gene of interest is generated by inserting a pair of FRT and FRT3 sites into the desired tagging locus. Fusion or co-expression tags from reusable tag donors can be efficiently swapped in the seed allele using Flp recombinase-mediated cassette exchange (RMCE). Furthermore, the tag-swapping step can be accomplished through simple genetic crossing, making it easy to scale up. We also built a library of plug-and-play tag donor strains that can be crossed with seed alleles to insert the corresponding tags. The TAG-IN strategy is highly efficient: a single seed allele for each tagging locus is needed to insert any tag of interest; a single tag donor strain can be used to swap the tag into any compatible seed allele. Thus, TAG-IN is a modular and combinatorial tool for efficient endogenous gene tagging in <i>C. elegans</i>, accelerating comprehensive functional studies.