Fig. 5: HSFA1a plays a major role in the dynamic formation of promoter-enhancer contacts in response to a heat stress. | Nature Communications

Fig. 5: HSFA1a plays a major role in the dynamic formation of promoter-enhancer contacts in response to a heat stress.

From: HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Fig. 5: HSFA1a plays a major role in the dynamic formation of promoter-enhancer contacts in response to a heat stress.The alternative text for this image may have been generated using AI.

a Phenotypes of WT and hsfa1a knock-down (via RNA interference) lines after 0 and 6 h of heat stress. b Expression level heatmap of genes that were down-regulated in two independent hsfa1a lines after 1 h of heat stress compared to the WT. c Gene ontology enrichment of down-regulated genes (n = 280). P-values calculated using Fisher’s exact test. d Pie chart representing the 247 HSFA1a target genes that were mis-regulated in hsfa1a lines after 1 h of heat stress compared to the WT. Among them, 75.3% were down-regulated in hsfa1a compared to the WT. e, g Screenshot of the Solyc09g074475 and HSFA2 locus. DAP-seq against Halo-tag and HSFA1 are represented in black and red. The RNA-seq, ATAC-seq and RNAPII ChIP-seq signal is represented in orange, blue and purple respectively. Chromatin interactions from C-Hi-C data and RNAPII HiChIP are represented by red and purple lines. The right green box of e shows a zoom of a distal RE that interacts with two heat stress-responsive genes (Solyc09g074475 and one non-annotated gene). The purple box of g shows a zoom of two distal REs named A and B that interact with HSFA2. The histogram represents the luciferase activity from a transient luciferase assay using a RE-mini35S::LUC construct or the mini35S::LUC alone as a control. The mean LUC/REN activity levels were normalized to mini35S::LUC as control (n = 3 biological replicates). f, h (Top) Design of the 3C-qPCR assays used to analyze the distal RE loops in the WT and hsfa1a lines in response to heat stress. (Bottom) Quantitative 3C; the relative interaction frequencies were calculated as described in the Materials and Methods. Data are the average of three biological replicates each with three technical replicates (n = 3). Circles in 5e, g denote relative LUC/REN activity values. Circles in e, f, g, h denote relative interaction frequency. Bars indicate mean values + /− SD of three replicates. Exact P-values are shown (two-tailed, two-sample Student’s t-test). Source data are provided as a Source Data file.

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