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Identification of the Genes Involved in Stomatal Development via Epidermal Phenotype Scoring

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Plastid perturbations trigger epigenetic programs during environmental sensing in plants.

Ha Eun Jeh^1,2, Isaac Dopp^1,2, Zizhang Li³

¹Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16802, United States.

Plant Physiology

|March 18, 2026

Summary

Plants use epigenetic modifications in sensory plastids to adapt to environmental changes. Perturbing these plastid proteins alters DNA methylation and gene expression, influencing plant responses to daylength and stress.

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Area of Science:

Plant Biology
Epigenetics
Environmental Sensing

Background:

Plants adapt to environmental changes via growth and defense adjustments, with epigenetic modifications playing a poorly understood role.
Specific plant tissues like epidermis and meristems possess sensory plastids crucial for environmental sensing and stress response.
Perturbation of sensory plastid proteins impacts plant epigenomes, gene expression, and DNA methylation patterns.

Purpose of the Study:

To investigate the effects of four sensory plastid-localized proteins (MSH1, PPD3, CUE1, SAL1) on the Arabidopsis epigenome.
To analyze gene expression and DNA methylation changes in response to environmental cues, particularly daylength.
To explore the interaction between sensory plastid mutants and the chromatin remodeler mutant hda6.

Main Methods:

Investigated effects of perturbing four sensory plastid proteins (MSH1, PPD3, CUE1, SAL1) on Arabidopsis epigenome.
Analyzed gene expression and DNA methylation changes, focusing on gene networks related to environmental sensing.
Compared effects at different daylengths (12-hr and 16-hr) and in combination with the hda6 mutant.

Main Results:

Sensory plastid protein perturbation caused DNA methylation and gene expression changes overlapping with those in the hda6 mutant at 12-hr daylength.
At 16-hr daylength, hda6 lost CHG hypermethylation, and sensory plastid mutants exhibited milder epigenetic and phenotypic adjustments.
Detected daylength-responsive epistatic interactions between sensory plastid mutants and hda6, with hda6 conferring daylength memory and enhanced stress tolerance.

Conclusions:

Sensory plastid-to-nucleus retrograde signaling epigenetically programs plant phenotypic adjustments in response to environmental cues like daylength.
Epigenetic modifications in sensory plastids are integral to plant adaptation strategies.
The study provides a model for understanding how plants integrate environmental signals through epigenetic mechanisms.