SRP345165 PRJNA778579 Arabidopsis thaliana 3D genome in PcG mutants and multiple conditions Higher-order chromatin organization is important to transcriptional regulation, genome stability, and other nuclear processes. Large differences have been observed in plants 3D chromatin organization relative to animals. The extent, pattern, and rules of chromatin organization in plants are unclear. Based on high-resolution Hi-C, we systematically identified long-range chromatin loops in cis and trans in Arabidopsis 3D genome. Their anchor regions are closely associated with H3K27me3, which suggested that Polycomb group (PcG) of proteins might involve in the establishment and maintenance of Arabidopsis 3D genome structure. Furthermore, based on Hi-C from PcG mutants, we confirmed that these chromatin loops depended on PRC2. We also found that the target genes of these chromatin loops are enriched in secondary metabolism pathway in plants. In Arabidopsis chromosome 4 and 5, we also identified interacting hubs occupied with high-level of H3K27me3 and embedded with metabolic gene clusters (MGCs) and tandemly arrayed gene cluster (TDGs). Compared with root Hi-C, we found long-range chromatin loop disappeared with increased gene expression of all genes within MGCs in aerial eventually. This phenomenon suggested that co-silencing model existed between two MGCs which were linear far from each other but close spatially. Moreover, PcG-mediated chromatin loops are dynamically regulated in aerial and root part of Arabidopsis, cold stressed, heat stressed, and auxin treated Arabidopsis. In other species like Oryza sativa, and Glycine max, we also identified similar PcG-associated chromatin loops, which indicated that the conservation of PcG-mediated loops in plants. More interestingly, we found high level of overlaps between their anchors and the two types of gene clusters. In summary, we utilized 3D genome approaches to identify PcG-mediated long-range chromatin loops and found their association with gene clusters. It provides novel insights to the genome evolution and transcriptional co-regulation. Arabidopsis thaliana cultivar:Col-0 pubmed 37154484