The democratization of gene editing: Insights from site-specific cleavage and double-strand break repair

Abstract

DNA double-strand breaks (DSBs) are dangerous lesions that if not properly repaired can lead to genomic change or cell death. Organisms have developed several pathways and have many factors devoted to repairing DSBs, which broadly occur by homologous recombination that relies on an identical or homologous sequence to template repair, or nonhomologous end-joining. Much of our understanding of these repair mechanisms has come from the study of induced DNA cleavage by site-specific endonucleases. In addition to their biological role, these cellular pathways can be co-opted for gene editing to study gene function or for gene therapy or other applications. While the first gene editing experiments were done more than 20 years ago, the recent discovery of RNA-guided endonucleases has simplified approaches developed over the years to make gene editing an approach that is available to the entire biomedical research community. Here, we review DSB repair mechanisms and site-specific cleavage systems that have provided insight into these mechanisms and led to the current gene editing revolution.

Initiation of homologous recombination at DNA nicks

“…The first of these was derived from the S. cerevisiae meganuclease, I-SceI, which had powered studies of the mechanism of DSB repair in S. cerevisiae itself and in mammals [reviewed by (53)]. Meganucleases, which are found in eukaryotes, archaea and bacteria, create DSBs at target sites 12–40 bp in length to produce recombinogenic ends bearing short 3′ overhangs that enable duplication of a mobile element by gene conversion (54).…”

Making complex things simpler: modern tools to edit the plant genome

“…1, а) (Савицкая и др., 2016). В клетках эукариот репарацию двуцепочечных разрывов обеспечи вают два основных механизма -NHEJ (nonhomologous end joining -негомологичное воссоединение концов) и HDR (homology directed repair -репарация на основе гомологичной рекомбинации) (Jasin, Haber, 2016). При репарации по типу NHEJ в месте разрыва могут проис ходить инсерции или делеции небольшой длины -до не скольких десятков пар нуклеотидов.…”

“…В случае, если требуется заменить эндогенную последовательность в геноме на экзогенную, необходим также третий компонент -донорная ДНК. Донорная ДНК содержит на 5′ и 3′конце последовательности ну клеотидов, идентичные участкам геномной ДНК, флан кирующим область вставки (Jasin, Haber, 2016). Процесс встраивания последовательностей в геном основан на рекомбинации между участком генома и экзогенной мо лекулой ДНК.…”

A Life Investigating Pathways That Repair Broken Chromosomes

“…The revelation of the past few years that virtually any sequence can be cleaved by using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 and an appropriate guide RNA has made it possible to efficiently knock out genes with small indels or, with less efficiency, to edit them by gene conversion (57). There are many exciting avenues to investigate beyond the question of how to make mammals more like yeast in gene-targeting efficiency (The best answer to this question is to reduce the genome complexity of a mammal!).…”