Single-cell epigenomics in plants

Single-cell technologies enable epigenomics characterization at single-cell resolution, offering novel insights into gene expression regulation and a wide range of biological processes, including cell fate determination, developmental differentiation, and environmental adaptation. In recent years, plant single-cell epigenomics has witnessed rapid progress, empowering the construction of cell type-specific chromatin accessibility atlases, the identification of candidate cis-regulatory elements (CREs), the inference of gene regulatory networks, and the elucidation of regulatory mechanisms underlying plant development, stress responses, species evolution, and complex agronomic traits. Nevertheless, single-cell methodologies for profiling histone modifications, DNA methylation, three-dimensional genome organization, and spatial epigenomic states in plants are still in their infancy. In this review, we systematically elaborate the technological framework, bioinformatic workflows, key research advances, and existing challenges in the field of plant single-cell epigenomics, and highlight future perspectives for its in-depth development.