Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis

Abstract

Stresses have been known to cause various responses like cellular physiology, gene regulation, and genome remodeling in the organism to cope and survive. Here, we assessed the impact of stress conditions on the chromatin-interactome network of Arabidopsis thaliana. We identified thousands of chromatin interactions in native as well as in salicylic acid treatment and high temperature conditions in a genome-wide fashion. Our analysis revealed the definite pattern of chromatin interactions and stress conditions could modulate the dynamics of chromatin interactions. We found the heterochromatic region of the genome actively involved in the chromatin interactions. We further observed that the establishment or loss of interactions in response to stress does not result in the global change in the expression profile of interacting genes; however, interacting regions (genes) containing motifs for known TFs showed either lower expression or no difference than non-interacting genes. The present study also revealed that interactions preferred among the same epigenetic state (ES) suggest interactions clustered the same ES together in the 3D space of the nucleus. Our analysis showed that stress conditions affect the dynamics of chromatin interactions among the chromatin loci and these interaction networks govern the folding principle of chromatin by bringing together similar epigenetic marks.

High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

“…S 2 ), similar to previous observations in rice in response to cold stress [ 12 ]. Interestingly, in Arabidopsis , it has been reported that heat stress induces long-range interactions but weakens short-range chromatin interactions [ 35 ]. These results suggest that cold and heat exert opposite effects on chromatin architecture, which might be intuitive as basic thermodynamics indicate that molecules expand with heat and contract with cold.…”

Three dimensions of thermolabile sex determination

“…New 3C‐based methods that permit the study of how genomes remodel in response to the environment at a fine scale (reviewed in Kumar et al. [ 36 ] ) have revealed that plant genomes can remodel in response to salicylic acid [ 37 ] and probably light (reviewed in Perrella et al. [ 38 ] ).…”

“…[33][34][35] Recently, the implications for direct 3D genome remodelling by temperature have also been considered. New 3C-based methods that permit the study of how genomes remodel in response to the environment at a fine scale (reviewed in Kumar et al [36] ) have revealed that plant genomes can remodel in response to salicylic acid [37] and probably light (reviewed in Perrella et al [38] ). In mammals (e.g., mouse liver), TADs that harbour circadian genes switch between active and inactive compartments at different times of the day, resulting in cycles of transcription modulation.…”

“…[40] However, in plants and yeast, gene expression changes induced by heat stress were coupled with modification to 3D genome structure. [37,41,42] In different Drosophila cells, heat stress induces a redistribution of architectural proteins that modulate TAD boundaries. [43] This chromatin remodelling, coupled with covalent his-tone modifications, promoted new long-range interactions that formed new enhancer-promoter contacts that affected gene expression.…”

Multi-omic dissection of ancestral heat stress memory responses inBrachypodium distachyon

“…Histone modifications are also crucial for thermotolerance (Zhao et al, 2020), as plants deficient in histone acetyltransferase GCN5 or histone deacetylase 6 ( HDA6 ) exhibit severe defects in thermotolerance under HS (Hu et al, 2015). Finally, HS has been shown to cause chromatin remodeling and change the 3D structure of the genome by altering the large-scale chromatin interactions (Yadav et al, 2022).…”