Functional & integrative genomicsNov 16, 2025

How changing plant gene activity works and its uses: current progress, challenges, and future outlook

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Jan 20, 2026

Abstract

Epigenome editing technology allows for programmable, heritable, and reversible control of gene expression in plants without altering the DNA sequence.

CRISPR/dCas9 systems, transcription activator-like effectors (TALEs), and zinc finger systems enable precise manipulation of DNA methylation and histone modifications.
These tools have been applied to key regulatory genes that influence flowering time, stress response, and crop yield.
Innovations such as SunTag, CRISPRoff/on, and RNA m6A editing represent significant advancements in the field.
New approaches have emerged in chromatin reprogramming, including locus-specific removal of certain chemical marks on histones.
Challenges remain in the delivery, off-target effects, and stability of transgenerational changes associated with these editing platforms.

Simplified

Epigenome editing has become a leading-edge technology of programmable, heritable and reversible control of gene expression in plants without changing the DNA sequence. CRISPR/dCas9 systems along with transcription activator-like effectors (TALEs) and zinc finger systems have made it possible to manipulate DNA methylation, histone modifications, and RNA epigenetic marks in a precise and locus-specific fashion. These tools have been used on major regulatory genes of flowering time, stress adjustment, and yield maximization in model and crop plants. This review synthesizes the current status of plant epigenome editing advances and highlights mechanistic innovations including SunTag, CRISPRoff/on and RNA m6A editing. It also emphasizes new paradigm shifts in chromatin reprogramming, including transcription-resistive chromatin states, locus-specific H3K27me3 demethylation, and nanobody-mediated chromatin targeting. Furthermore, it considers the consequences of these shifts in the context of trait stability and epigenetic inheritance. Moreover, the relative evaluation of dCas9-, TALE-, and ZFP-based platforms indicated that there are still enduring problems in the performance of delivery, off-target effects, and transgenerational stability. The review concludes with a conceptual framework connecting epigenome editing to climate-smart crop improvement and outlines future research priorities focused on combinatorial multi-omics integration and the development of environmentally responsive editing platforms.

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Declarations. Competing interests: The authors declare no competing interests.

PubMed

How changing plant gene activity works and its uses: current progress, challenges, and future outlook

Abstract

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You found one interesting study. We’ll send the next 7.

What Lands in Your Inbox Each Week:

Recent issues from the crispr gene editing brief