• We established a comprehensive multi-omics dataset integrating time-course RNA-seq, Hi-C, and CUT&Tag analyses from two cotton genotypes. • This study presents the first systematic delineation of multi-scale 3D genome reorganization in plants under biotic stress. • GhGLR4.8, which encodes a glutamate-receptor-like protein that functions as an atypical resistance gene and a major calcium channel, orchestrates redistribution of epigenomic landscapes. Its mediated chromatin state and intra-chromatin interaction exhibit temporal and subgenome-specific divergence during immune responses. • GhGLR4.8 interacts with calmodulins to propagates calcium signals downstream. • This study valuable insights into how Ca 2+ signaling regulates chromatin structure dynamics and epigenetic modification states of immune-related genes. Plants evolve sophisticated strategies to rapidly regulate gene expression in response to environmental stress. Epigenetic regulation and highly dynamic three-dimensional (3D) chromatin reorganization are critical mechanisms mediating transcriptional reprogramming under stress conditions. However, to what extent biotic stress induces chromatin reorganization and the underlying mechanisms remain inadequately understood. This study aims to investigate how Fusarium oxysporum f. sp. vasinfectum ( Fov ) triggers reorganization of higher-order chromatin architecture and epigenetic modifications in cotton, and to elucidate the role of the resistance gene GhGLR4.8 in regulating these dynamic multi-omic responses during plant immunity. we established a comprehensive multi-omics dataset integrating time-course transcriptomic, epigenomic (H3K27ac/H3K27me3), and 3D genomic ( in situ Hi-C) data from wild-type cotton plants and GhGLR4.8 knockout mutants. The study demonstrated that Fov stress impacts multiscale 3D genome reorganization, including transitions in A/B compartments, rearrangements of topologically associated domains (TADs) and rewiring of chromatin loops. These chromatin architectural changes correlated with alterations in H3K27me3 and H3K27ac states, as well as transcriptional reprogramming of defense-related genes. GhGLR4.8 deficiency profoundly perturbed these multi-omic landscapes. Comparative analysis showed that GhGLR4.8 knockout elevated transition frequency between H3K27me3 and H3K27ac chromatin states and disrupted TAD-like domain rearrangements within immune-related genomic regions. Rearranged TAD boundaries exhibited markedly differential transcription factor enrichment between the two genotypes. Furthermore, Knocking down GhCaM1 , a gene encoding calmodulin and an interacting partner of GhGLR4.8 , compromised cotton resistance to Fov and attenuated the ROS burst. This study uncovered higher-order chromatin architecture as a new layer for transcriptional regulation during cotton immune response, expanding our knowledge of the mechanisms underlying transcriptional regulation in response to biotic stress in plants.
Liu et al. (Sun,) studied this question.