Epigenetic silencing is a barrier to editing the X chromosome using the SEC-based CRISPR/Cas9 knock-in protocol in C. elegans

Self-excising-cassette (SEC)-based CRISPR/Cas9 knock-in is widely used for generating endogenous fluorescent protein tags in <i>C. elegans</i> . Here, we report a lack of success targeting the X chromosome using this method. CRISPR/Cas9 works as intended, but subsequent floxing of the SEC is blocked. Given that the X chromosome is epigenetically silenced in primordial germ cells (PGCs), this is a logical result. To circumvent this barrier, we suppressed polycomb repressive complex 2 (PRC2) with RNAi to transiently and reversibly reduce silencing in the PGCs, creating a brief window where the X chromosome is amenable to floxing without compromising germ line development. Overall, our results reveal a previously unrecognized limitation of SEC-based CRISPR/Cas9 knock-in and identify a reliable workaround for tagging proteins encoded on the X chromosome.