Single-cell epigenomics in plants.

Plant single-cell epigenomics is rapidly advancing, enabling cell type–specific chromatin accessibility atlases and CRE discovery, but profiling histone modifications, DNA methylation, 3D genome organization, and spatial epigenomic states remains in its infancy.

• Why it matters: The field addresses a gap in plant epigenome mapping at single-cell resolution, which is needed to better understand how gene regulation shapes development, stress responses, evolution, and agronomic traits.
• What they did: The review systematizes the technological framework and bioinformatic workflows, summarizing advances such as cell type–specific chromatin accessibility atlases, candidate cis-regulatory element identification, gene regulatory network inference, and regulatory mechanism elucidation.
• The result: It consolidates current capabilities and challenges, outlining future perspectives to accelerate deeper plant single-cell epigenomic profiling beyond chromatin accessibility.

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