Advances in genome editing technology and its promising application in evolutionary and ecological studies

Abstract

Genetic modification has long provided an approach for "reverse genetics", analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace with the soaring progress of the genome sequencing era, as a result of their inefficiency, time-consuming and labor-intensive methods. Recently, invented genome modification technologies, such as ZFN (Zinc Finger Nuclease), TALEN (Transcription Activator-Like Effector Nuclease), and CRISPR/Cas9 nuclease (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 nuclease) can initiate genome editing easily, precisely and with no limitations by organism. These new tools have also offered intriguing possibilities for conducting functional large-scale experiments. In this review, we begin with a brief introduction of ZFN, TALEN, and CRISPR/Cas9 technologies, then generate an extensive prediction of effective TALEN and CRISPR/Cas9 target sites in the genomes of a broad range of taxonomic species. Based on the evidence, we highlight the potential and practicalities of TALEN and CRISPR/Cas9 editing in non-model organisms, and also compare the technologies and test interesting issues such as the functions of candidate domesticated, as well as candidate genes in life-environment interactions. When accompanied with a high-throughput sequencing platform, we forecast their potential revolutionary impacts on evolutionary and ecological research, which may offer an exciting prospect for connecting the gap between DNA sequence and phenotype in the near future.

Keywords: Domestication; Genetic innovations; Genetic modification; Life-environment interaction.

Figure 1

Mechanism of ZFN, TALEN and CRISPR/Cas9. A. ZFN, TALEN and CRISPR/Cas9 achieve precise and efficient genome modification by inducing targeted DNA DSBs, which would be corrected by NHEJ and HR repair mechanisms. NHEJ-mediated repair leads to the introduction of variable length insertion or deletion. HR-mediated repair could lead to point mutation and gene replacement, in the present of donor DNA. B. TALEs and Cas9 protein fused with effector proteins such as VP64, Mxi1 could regulate expressions of endogenous genes. Additionally, TALEs fused with histone-deacetylating epigenetic effectors could regulate epigenetics status of endogenous genes. CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats; dCas9, inactive Cas9 protein; DSB, Double Strand Breaks; NHEJ, Error-prone Nonhomologous End Joining; HR, Homologous Recombination; InDel, Insertion and Deletion; PAM, Protospacer Adjacent Motif; RNA Pol II, RNA Polymerase II; sgRNA, single guide RNA; TALE, Transcription Activator-Like Effector; TALEN, Transcription Activator-Like Effector Nuclease; ZFN, Zinc Finger Nuclease.