The plant specific cohesin subunit SYN4 contributes to 3D genome organization and activity

Chromatin architecture in the cells of animals and fungi influences gene expression. The molecular factors that influence higher genome architecture in plants and their effects on gene expression remain unknown. Cohesin complexes, conserved in eukaryotes, are essential factors in genome structuring. Here, we investigated the relevance of the plant-specific somatic cohesin subunit SYN4 for chromatin organisation in Arabidopsis thaliana. Plants mutated in SYN4 were studied using HRM, Hi-C, RNA sequencing, untargeted and targeted metabolomics and physiological assays to understand the role of this plant-specific cohesin. We show that syn4 mutants exhibit altered intra- and interchromosomal interactions, expressed as sharply reduced contacts between telomeres and chromosome arms but not between centromeres, and differences in the placement and number of topologically associated domain (TAD)-like structures. By transcriptome sequencing, we also show that syn4 mutants have altered gene expression, including numerous genes that control abiotic stress responses. The response to drought stress in Arabidopsis is strongly influenced by the genome structure in syn4 mutants, potentially due to altered expression of CYP707A3, an ABA 8'-hydroxylase.