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.
Highlights
The haploid A. thaliana genome contains approximately 125 million base pairs of DNA packaged into five chromosomes (Kaul et al, 2000)
The present study aims at understanding the dynamics of chromatin interaction during stress conditions, high temperature (HT) representing abiotic stress and salicylic acid (SA) mimic biotic stress was selected to capture chromatin interactions
We have identified that A. thaliana genome can be partitioned into two broad groups based on the correlation of interacting reads (Figure 1C) (Lieberman-Aiden et al, 2009; Sexton et al, 2012; Yadav et al, 2021)
Summary
The haploid A. thaliana genome contains approximately 125 million base pairs of DNA packaged into five chromosomes (Kaul et al, 2000). That makes a total 250 million base pairs of DNA in a single diploid cell of A. thaliana, which spans a total length of ∼8.5 cm. This stretch of DNA is approximately 16,000 times larger than the diameter of A. thaliana nucleus (Dittmer et al, 2007). Loop formation is an integral part of chromatin organization which facilitates interactions between distal genomic elements (Deng et al, 2012; Sandhu et al, 2012)
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