Layered regulation of plant 3D chromatin architecture by histone marks, transcription factors and cohesin‑mediated loops

The three-dimensional (3D) organization of the genome has emerged as a central layer of gene regulation in eukaryotes. In plants, chromatin architecture displays both conserved features and lineage-specific characteristics, reflecting differences in genome composition, epigenetic landscapes and regulatory strategies. Recent evolutionary analyses suggest that plants preferentially adopt a chromosome-scale "global folding" strategy distinct from the compartmentalized architecture observed in animals, which raises an important question: how is regulatory information coordinated in plants in the absence of canonical architectural proteins such as CCCTC-binding factor (CTCF) and strong compartmental domains? Here, we discuss evidence supporting a model in which plant 3D genome organization arises from the interplay between three major regulatory layers: chromatin states defined by histone modifications, transcription factor-mediated regulatory interactions, and cohesin-dependent chromatin extrusion. We further propose that these mechanisms operate within a global folding framework that balances structural stability with regulatory plasticity.