Fig. 6: Chromatin organization rearrangement revealed by high-resolution Hi-C correlates with heat-induced TE expression.

a, b Changes of local chromatin organization and TE expression at KEE3 and KEE4 loci after heat treatment. Two 100 kb regions (depth: 50 kb) containing KEE3 and KEE4, respectively, are shown. The top panels are heatmaps showing natural logarithm of 1 kb Knight and Ruiz (KR) normalized contact frequency in Control and Heat. Below are heatmaps (O/E) showing natural logarithm of observed/expected contact frequency in Control and Heat at 1 kb resolution. Below are heatmaps showing TAD-separation scores at different window sizes for each Hi-C genomic bin in Control and Heat. Loops were collected and transformed from a previous study (“Methods”). TE expression track shows the expression levels of TEs in Control and Heat. Their expression levels in Control and Heat are under the same scale and overlayered together. Only TE expression is shown. The expression of PCGs is not shown (“Methods”). The expanded panels show TE expression and the corresponding chromatin loops over KEE3 and KEE4. c Metagene plot of TAD-separation scores over bodies of heat-activated TEs and total TEs and flanking regions. Only TEs with length over 1,000 bp are considered. TSS transcription start site, TTS transcription termination site. d Heatmap of TAD-separation scores over bodies of 263 heat-activated TEs and flanking regions in Control. e Local rescaled pileup of chromatin organization over bodies of heat-activated TEs (upper panel) and total TEs (lower panel) in Control, Heat, and different biological replicates. The values are normalized by a local background (“Methods”). The diagonal bars are the locations of scaled heat-activated TEs (upper panel) and total TEs (lower panel). f Metagene plot of RNA-Seq read coverage over bodies of heat-activated TEs in Control, Heat, and Recovery. Heat stress can activate heterochromatin-associated transposon elements (TEs). Here, the authors show that heat stress leads to global rearrangement of 3D genome and TEs activation closely correlates with 3D chromatin organization rearrangement in Arabidopsis.