Plant gene expression control using genome- and epigenome-editing technologies

In this review, we present some specific examples of plant species only where modulation of gene regulation has been achieved via genome-editing and epigenome-editing technologies. Among genome-editing tools used in plants are zinc-finger nucleases in maize (Zea mays L.); transcription activator-like effector nucleases in rice (Oryza sativa L.), sugarcane (Saccharum spp.), and wheat (Triticum aestivum L.); and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) in O. sativa and tomato (Solanum lycopersicum L.). A large number of epigenome-editing tools based on small RNAs have been employed for controlling plant gene expression in thale cress (Arabidopsis thaliana), tobacco (Nicotiana benthamiana), O. sativa, potato (Solanum tuberosum), and Z. mays. RNAi-based tools have been used in A. thaliana; RNA-directed DNA Methylation (RdDM) in A. thaliana; and RdDM involving transgenically produced exogenous small interfering RNAs in O. sativa. Site-specific DNA-binding proteins that have been successfully repurposed to function as DNA-binding domains of epigenome-editing tools include zinc-finger proteins, transcription activator-like effectors, and dead Cas9 complexed with single-guide RNA. Zinc-finger-based epigenome-editing tools have been applied in A. thaliana and O. sativa; and transcription activator-like effector and dead Cas9-based tools in O. sativa and A. thaliana, respectively. Targeting-induced-local-lesions-in-genomes approach has been employed in muskmelon (Cucumis melo). Quantitative trait loci (QTL) were epigenetically modified in A. thaliana and O. sativa. In vitro tissue culture-based epigenome-editing DNA and/or histone modifications have been achieved in Caribbean agave (Agave angustifolia), Henequen (Agave fourcroydes), A. thaliana, common tobacco (Nicotiana tabacum), O. sativa, pine (Pinus radiata), and Z. mays.