Fig. 6: Hi-C analysis demonstrates the more compact state of active chromatin and the decompactization of inactive chromatin upon Elys-KD.

a A schematic showing TADs and compartments. b Hi-C heatmap for the representative region of 3L chromosome in Elys-KD (above the diagonal) and control (below the diagonal) cells. TADs (demarcated by black dotted lines), RNA-seq profile in control cells (in RPM, blue peaks), RefSeq genes, and chromatin annotation in S2 cells according to the 9-state model are indicated below the Hi-C map. c Box-plots showing log₂FC of ACF (Elys-KD/control) for TADs divided into three groups (A, B, C). Black lines represent median values, upper and lower ends of box-plot show the upper and lower quartiles, the whiskers indicate the maximum and minimum values, and individual points show the outliers. P-values were estimated in a Wilcoxon signed-rank test. d Saddle-plot showing subtraction of aggregated contact frequency (Elys-KD minus control) log₂FC(observed/expected) for autosomes. Dashed lines indicate areas that were analyzed on (e). e Box-plots showing subtraction of aggregated contact frequency (Elys-KD minus control) log₂FC(observed/expected) for autosomes within active (AA), inactive (BB), and between active and inactive (AB) chromatin compartments. Black lines represent median values, upper and lower ends of box-plot show the upper and lower quartiles, the whiskers indicate the maximum and minimum values, and individual points show the outliers. P-values were estimated in a Wilcoxon signed-rank test. f, g Heatmaps showing subtraction of ACF (Elys-KD minus control) log₂FC(observed/expected) around Elys_NPC sites located in the inactive chromatin (states 6-9) (f) or around Elys_nucl sites containing > 50% of active chromatin (states 1 and 2) (g). h, i Averaged IS^m profiles around Elys_NPC sites located within inactive (states 6–9) chromatin (h) or around Elys_nucl sites (i) in control (blue curve) and Elys-KD (red curve) cells. IS^m profiles were calculated for 2-kb resolution Hi-C heatmaps. Only contacts between regions located 2–8 kb away from both sides of the central bin were considered. j A schematic showing how the attachment to NPCs may facilitate contacts between regions located on both sides from the Elys_NPC site.