The CRISPR-dCas9 epigenetic toolbox: prospects for modulating gene expression in climate-resilient crops

CRISPR-dCas9 epigenome editing represents a paradigm shift from static DNA sequence editing to dynamic reprogramming of gene expression, offering a powerful and precise toolbox with the potential to develop stable and climate-resilient crops without altering DNA sequences. The escalating challenges of global food security, driven by climate change and population growth, necessitate innovative crop improvement strategies that extend beyond conventional breeding. Although CRISPR-Cas9 has revolutionized plant biotechnology through direct genome editing, CRISPR-based epigenome editing has emerged as a new frontier. By repurposing nuclease-dead Cas9 as a programmable targeting platform fused to epigenetic effector domains, researchers can precisely modulate gene expression without altering the DNA sequence. This approach has already yielded compelling successes, such as the engineering of durable resistance to cassava bacterial blight through targeted epigenetic silencing of a susceptibility gene. This review focuses primarily on the current state of CRISPR-based epigenome editing systems, including acetyltransferases, demethylases, DNA methyltransferases, and deacetylases, and their applications in crop improvement research. We critically evaluate their mechanisms in rewriting epigenetic regulatory information, their demonstrated efficacy in enhancing yield components, disease resistance, and abiotic stress tolerance, and their potential to create stable meiotically heritable epialleles, although most demonstrations remain at the proof-of-concept stage in model plants, with field validation in major crops still limited. This review provides a balanced analysis of key challenges, including editing specificity, context-dependency, delivery limitations, and regulatory considerations. Finally, we outline future directions focusing on technological refinement, multi-omics integration, and field validation. Epigenome editing shows promise as a conceptually distinct and transformative approach in crop biotechnology, through targeted modulation of a plant's epigenetic landscape. However, its full potential hinges on overcoming challenges related to stability, predictability, and field-scale validation.