In eukaryotes, topologically associating domains (TADs) organize the genome into functional compartments. While TAD-like structures are common in mammals and many plants, they are challenging to detect in Arabidopsis thaliana. Here, we demonstrate that Arabidopsis PDS5 proteins play a negative role in TAD-like domain formation. Through Hi-C analysis, we show that mutations in PDS5 genes lead to the widespread emergence of enhanced TAD-like domains throughout the Arabidopsis genome, excluding pericentromeric regions. These domains exhibit increased chromatin insulation and enhanced chromatin interactions, without significant changes in gene expression or histone modifications. Our results suggest that PDS5 proteins are key regulators of genome architecture, influencing 3D chromatin organization independently of transcriptional activity. This study provides insights into the unique chromatin structure of Arabidopsis and the broader mechanisms governing plant genome folding. Topologically associating domain (TAD) facilitates the creation of distinct chromatin compartments and specific chromatin interaction, but TAD-like structures are lacking in Arabidopsis. Here, the authors report the possible role of PDS5s in suppressing the formation of TAD-like domains in Arabidopsis.

One key structural element in the three-dimensional (3D) chromatin organization is the Topologically Associating Domain (TAD), which facilitates the formation of distinct chromatin compartments and fosters specific chromatin interactions. Similar chromatin compartments, known as TAD-like domains, have been identified in many plant species. However, the model plant Arabidopsis thaliana has been an exception. In this study, we address this long-standing issue by presenting evidence that Arabidopsis PDS5 proteins play a crucial role in preventing the formation of TAD-like domains. ### Competing Interest Statement The authors have declared no competing interest.

The nuclear lamina is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. In Arabidopsis thaliana , nuclear matrix constituent proteins (NMCPs) are essential components of the nuclear lamina and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein-coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei is flexible and responds to various developmental cues and environmental stimuli. On the basis of these observations in Arabidopsis , and given the role of NMCP genes ( CRWN1 and CRWN4 ) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin–nuclear lamina interactions when the global chromatin organization patterns are being altered in plants. Here we report the highly flexible nature of the plant nuclear lamina, which disassembles substantially under various stress conditions. Focusing on heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. By investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional coregulator to modulate the shift of the plant transcriptome profile in response to heat stress.