PDS5A restricts SYN4-dependent long-range chromatin contacts to shape TAD-like chromatin architecture in Arabidopsis

Three-dimensional genome folding in vertebrates, such as the formation of topologically associating domains (TADs), depends on cohesin-mediated loop extrusion, yet its regulation in plants remains unresolved. Using Hi-C and Micro-C, here we show that Arabidopsis cohesin regulator PDS5A is a key modulator of chromatin loop extrusion and TAD-like architecture. The TAD-like domain patterns in pds5a are highly similar across tissues and ploidy levels. Genetic evidence reveals that TAD-like domains require the plant kleisin SYN4 and are opposed by WAPL1/2, with PDS5A serving as the major cohesin-unloading factor. Biochemical assays show that PDS5A associates with cohesin independently of its Tudor domain-mediated H3K4me1 binding. Micro-C further identifies accessible, highly transcribed promoters as chromatin loop and stripe anchors. Finally, mutational disruption of distal chromatin anchors shows that newly formed chromatin contacts in pds5a can act as cis-regulatory modules that influence target gene expression. Together, these findings identify a PDS5A-regulated chromatin extrusion module that contributes to plant 3D genome organization and uncover a promoter-based logic for loop anchoring and transcriptional control in plants.