HOMEODOMAIN-LIKE shapes chromatin architecture and rewires leaf epidermal patterns

Abstract

During development, cells balance proliferation and differentiation to generate diverse cell types, yet how these transitions are fine-tuned remains unclear. In the Arabidopsis leaf epidermis, stomata form through regulated cell division, whereas pavement cells and trichomes arise through differentiation, making this tissue a tractable system for identifying modulators of developmental decisions. Here, we identified a previously uncharacterized homeodomain-like protein HDL, that is required for chromocenter organization through interactions with the histone deacetylase HDA6 and the methyltransferase KRYPTONITE. hdl mutants exhibit disrupted chromocenters and reduced cell division, resulting in fewer stomata and increased trichome formation. Chromatin immunoprecipitation and ATAC-sequencing reveal increased chromatin accessibility at HDL-associated regions and reduced accessibility and expression of stomatal lineage–related genes. Chromatin-state and H3K9me2 analyses further suggest that HDL functions as a chromatin organizer that maintains epigenetic balance at the interface between active and repressive chromatin domains, thereby shaping genome-wide transcriptional programs. Together, these findings identify HDL as a chromatin-associated factor linked to coordinated changes in chromocenter architecture and developmental plasticity. How chromatin organization influences developmental decisions remains poorly understood. Here the authors report a chromatin organizer that maintains higher-order genome organization and coordinated gene expression to balance cell division and differentiation in plants.