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

Abstract

SummaryChromatin 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 inArabidopsis thaliana.Plants mutated inSYN4were 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 thatsyn4mutants 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 domains (TADs)-like structures. By transcriptome sequencing, we also show thatsyn4mutants have altered gene expression, including numerous genes that control abiotic stress responses.The response to drought stress inArabidopsisis strongly influenced by the genome structure insyn4mutants, potentially due to altered expression ofCYP707A3, an ABA 8’-hydroxylase.In briefThe 3D architecture of the genome extensively influences gene expression in animals and fungi. We show that the plant-specific cohesin subunit SYN4 affects intra- and interchromosomal interactions including telomere clustering, with consequences for the expression of genes of transient and induced biological pathways and the biosynthesis of bioactive compounds. Highly condensed genome structures at theCYP707A3locus positively affects the stress response to water deprivation regulated by abscisic acid.