Gene editing tools: state-of-the-art and the road ahead for the model and non-model fishes

Abstract

Advancements in the DNA sequencing technologies and computational biology have revolutionized genome/transcriptome sequencing of non-model fishes at an affordable cost. This has led to a paradigm shift with regard to our heightened understandings of structure-functional relationships of genes at a global level, from model animals/fishes to non-model large animals/fishes. Whole genome/transcriptome sequencing technologies were supplemented with the series of discoveries in gene editing tools, which are being used to modify genes at pre-determined positions using programmable nucleases to explore their respective in vivo functions. For a long time, targeted gene disruption experiments were mostly restricted to embryonic stem cells, advances in gene editing technologies such as zinc finger nuclease, transcriptional activator-like effector nucleases and CRISPR (clustered regulatory interspaced short palindromic repeats)/CRISPR-associated nucleases have facilitated targeted genetic modifications beyond stem cells to a wide range of somatic cell lines across species from laboratory animals to farmed animals/fishes. In this review, we discuss use of different gene editing tools and the strategic implications in fish species for basic and applied biology research.

Editing the duplicated insulin-like growth factor binding protein-2b gene in rainbow trout (Oncorhynchus mykiss)

“…Understanding the functional roles of the IGFBP subtypes will be critical to establish their specific roles as modulators of IGF signaling and loss-of-function studies are critical to identify these protein-level functions. Advancements in gene editing technology, particularly using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system, has expanded the capacity for targeted gene mutagenesis in many animals, including fish 35 , 36 . This technology has been successfully performed in several aquacultured species, including Atlantic salmon 37 , 38 , catfish 39 , 40 , tilapia 41 , 42 , and carp 43 , 44 to induce a range of phenotypes related to fertility, muscle growth, and disease resistance.…”

Status of genetic and genomic approaches for delineating biological information and improving aquaculture production of farmed rohu, Labeo rohita (Ham, 1822)

“…Cutting‐edge genome editing technologies such as zinc finger nuclease (ZFN), transcriptional activator‐like effector nucleases (TALENs) and CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 can be utilized for generating transgenic fish via homologous recombination mechanism (Zhu & Ge, 2018). It has been depicted that, precise gene/genome editing could be possible in fish species (Barman et al, 2017; Gratacap et al, 2019). CRISPR‐Cas9 can then be used to execute gene knock‐in or knock‐out to further investigate the functions of genes, transcripts and microRNAs, which will help to resolve transgenic efficiency issues.…”

Biotechnological innovation in genetic breeding and sustainable green development in Chinese aquaculture

“…在基因组编辑技术方面, ZFNs(zinc finger nucleases) [140] , TALENs(transcription activator-like effector nucleases) [141] 和CRISPR/Cas9(clustered regularly interspaced short palindromic repeats/Cas9) [142,143] [65,102,147,148] . 2014年, 中国学者领 衔完成了"斑马鱼1号染色体全基因敲除计划", 敲除了 斑马鱼1号染色体上的1333个基因, 为建立水产育种学 模型等研究奠定了基础 [65,145,149] .…”