Bacterial Memory to Genome Surgery: A Narrative Review of the CRISPR Systems, from Repeated Sequences to Prime Editing

Abstract

CRISPR is biology's most improbable technology: a bacterial adaptive immune system, recognized only gradually from odd repeated sequences in microbial genomes, became within a decade the universal tool of genome editing---Cas9's programmable double-strand cuts, the Cas12 and Cas13 families' extensions, and prime editing's search-and-replace precision. This article presents a narrative review of the primary literature of that transformation, from Ishino and colleagues' nucleotide sequence of the iap gene, where the repeats were first recorded, through the biological decipherment: Mojica and colleagues' biological significance of the regularly spaced repeats, Bolotin and colleagues' spacers of extrachromosomal origin, and Barrangou and colleagues' demonstration that CRISPR provides acquired resistance against viruses---the system's function proven, Wiedenheft, Sternberg, and Doudna's synthesis of the RNA-guided silencing, and the engineering program: Jinek, Chylinski, Fonfara, Hauer, Doudna, and Charpentier's programmable dual-RNA-guided endonuclease---Cas9 harnessed---Cong and colleagues' and Mali and colleagues' multiplex engineering in human cells, Doudna and Charpentier's frontier review, Zetsche and colleagues' Cpf1 as the compact Cas12, Abudayyeh and colleagues' C2c2 as the RNA-targeting Cas13, and Anzalone and colleagues' prime editing---search-and-replace without double-strand breaks. The synthesis is organized around three themes: the curiosity phase, in which the repeats' function was decoded from bioinformatics to immunity; the engineering phase, in which the bacterial nuclease became a programmable editor; and the diversification phase, in which the Cas families' variety---DNA and RNA targeting, base and prime editing---built the editing toolkit. It is concluded that CRISPR is the paradigm case of curiosity-driven microbiology becoming world technology, and that its systems' continued natural diversity remains the source of its future.