High Efficiency, Homology-Directed Genome Editing in <i>Caenorhabditis elegans</i> Using CRISPR-Cas9 Ribonucleoprotein Complexes

TLDR

HDR of Cas9‑induced breaks is a widely used genome‑editing strategy, but most protocols rely on plasmid‑based expression of Cas9 and guide RNAs. We devised a cloning‑free protocol that injects Cas9‑crRNA‑tracrRNA ribonucleoprotein complexes into the C. elegans gonad and uses PCR fragments with 35‑base homology as seamless repair templates.

Abstract

Abstract Homology-directed repair (HDR) of breaks induced by the RNA-programmed nuclease Cas9 has become a popular method for genome editing in several organisms. Most HDR protocols rely on plasmid-based expression of Cas9 and the gene-specific guide RNAs. Here we report that direct injection of in vitro–assembled Cas9-CRISPR RNA (crRNA) trans-activating crRNA (tracrRNA) ribonucleoprotein complexes into the gonad of Caenorhabditis elegans yields HDR edits at a high frequency. Building on our earlier finding that PCR fragments with 35-base homology are efficient repair templates, we developed an entirely cloning-free protocol for the generation of seamless HDR edits without selection. Combined with the co-CRISPR method, this protocol is sufficiently robust for use with low-efficiency guide RNAs and to generate complex edits, including ORF replacement and simultaneous tagging of two genes with fluorescent proteins.