Advances in Plant Epigenome Editing Research and Its Application in Plants

Abstract

Plant epistatic regulation is the DNA methylation, non-coding RNA regulation, and histone modification of gene sequences without altering the genome sequence, thus regulating gene expression patterns and the growth process of plants to produce heritable changes. Epistatic regulation in plants can regulate plant responses to different environmental stresses, regulate fruit growth and development, etc. Genome editing can effectively improve plant genetic efficiency by targeting the design and efficient editing of genome-specific loci with specific nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9). As research progresses, the CRISPR/Cas9 system has been widely used in crop breeding, gene expression, and epistatic modification due to its high editing efficiency and rapid translation of results. In this review, we summarize the recent progress of CRISPR/Cas9 in epigenome editing and look forward to the future development direction of this system in plant epigenetic modification to provide a reference for the application of CRISPR/Cas9 in genome editing.

Keywords: CRISPR/Cas9; epistatic regulation; genome editing; plant.

Figure 1

Application of CRISPR in plant epigenetic regulation (by Biorender). (A) CRISPRi inhibits the transcription of target DNA by forming a steric hindrance through the targeted binding of dCas9-sgRNA complex to target DNA. Piatek et al. fused the C-terminus of dCas9 to the transcriptional repressor domain of SRDX and successfully suppressed the transcription of endogenous genes in plant cells [32]. In addition, D144, DLS, and MIX were also successfully verified in monocotyledonous plant wheat to inhibit transcriptional activity [33]. (B) Activation of specific gene expression can be achieved by fusion of dCas9 with transcriptional regulators such as VP64 and EDLL. The expression of chimeric d Cas9: EDLL and d Cas9: TAD transcriptional activators in N. benthamiana can activate the expression of target gene PDS, and different transcriptional activators need to target different distances from TSS to obtain the best transcriptional activation level [32]. The dCas9-VP64 coupled with MS2-VP64 via gRNA2.0 constitutes a new system CRISPR-Act2.0, which successfully performed robust and multiple activation of three genes Os03g01240, Os04g39780 and Os11g35410 in rice [34]. (C) The CRISPR-Cas9 SunTag NtDRMcd system was used to methylate the specific site of FWA promoter in Arabidopsis, which successfully inhibited the expression of FWA and caused early flowering phenotype in Arabidopsis [35]. (D) The dCas9 was fused with an Arabidopsis histone acetyltransferase 1, histone acetylation causes structural changes in chromatin and promotes the assembly of transcription mechanisms, resulting in enhanced gene transcription and subsequent protein accumulation. The AREB1 overexpression promotes an improvement in the physiological performance of the transgenic homozygous plants under drought [36].