Genome editing using CRISPR-Cas
Hyongbum (Henry) Kim, Yonsei University College of Medicine
Programmable nucleases, which include zinc-finger nucleases, transcriptional activator-like effector nucleases, and RNA-guided engineered nucleases derived from the prokaryotic CRISPR/Cas system, enable targeted genetic modifications in cultured cells, animals, and plants, tools of great value in research, medicine, and biotechnology. Cpf1 is a recently reported effector endonuclease protein of the class 2 CRISPR-Cas system. Cpf1 has several differences from Cas9: cleavage with 5’ overhangs, shorter guide RNA, and a longer distance between the seed sequence and cleavage site, which could provide potential advantages for some cases of genome editing such as nonhomologous end joining-based gene insertion and efficient genome editing using homology-directed repair. However, limited information is available about Cpf1 activity profiles in mammalian cells, precluding its wide use for genome editing. Here, we performed en masse evaluation of guide RNA and Cpf1 activity using synthetic target sequences and deep sequencing. Using this approach, we determined target sequence-dependent activity profiles and protospacer adjacent motif sequences of Cpf1. We found that sequence features of high activity AsCpf1 guide RNAs are distinct from those of SpCas9. Evaluation of activity at mismatched target sequences showed that Cpf1 target sequences can be divided into seed, trunk, and promiscuous regions depending on mismatch tolerability. The Cpf1 characterization profile will greatly facilitate Cpf1-based genome editing.