Rapidly evolving genome and epigenome editing technologies

Abstract

Genome editing technologies are rapidly evolving, from the early zinc-finger nucleases, transcription activator-like effector nucleases (TALENs), and CRISPR-Cas9 (Figure 1, initial genome editing technologies), which generate double-strand breaks (DSBs), to base editing, which makes precise nucleobase conversion without inducing DSBs, and prime editing, which can carry out all types of edits without DSBs or donor DNA templates. The emergence of these revolutionary technologies offers us unprecedented opportunities for biomedical research and therapy development.

Figure 1

Evolving genome and epigenome editing technologies Initial genome editing technologies: all first-generation genome editors, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR-Cas9, generate double-strand DNA breaks (DSBs). Prime editing: prime editing (PE) efficiency can be improved by modulating nucleotide metabolism and machine learning to predict the prime editing guide RNA (pegRNA). VPX, an accessory lentiviral protein, mediates the degradation of SAMHD1. SAMHD1 is a triphosphohydrolase responsible for dNTP depletion, which is a limiting factor of reverse transcriptase (RT)-dependent PE. RNA-guided recombinase system: bridge RNA containing a target-binding loop and donor-binding loop directs recombinase (IS621) to both target and donor sequences via the core sequence (Core seq), thus mediating recombination. LTG, left targeting guide; RTG, right targeting guide; LDG, left donor guide; RDG, right donor guide; RE, right element; LE, left element. ZFcharm epigenome editing: a compact Epi-editor, ZFcharm (including ZFN, AsD3L, and an H3 tail), fits into a single AAV and is designed to bind to the Prnp promoter, recruit endogenous DNMT3A, and methylate the CpG islands, thus leading to long-term suppression of Prnp in vivo. This figure was created with BioRender.com. The part “Initial genome editing technologies” was adapted from a BioRender.com template titled Mechanism of Genome Editing Tools, which was created by Wendy Jiang.