Fig. 8: Depletion of H3K36me results in decreased nuclear compartmentalization.
From: H3K36 Methylation as a Guardian of Epigenome Integrity
a Hi-C heatmaps illustrating reduced nuclear compartmentalization in QuiKO mMSCs. b Saddleplots showing decreased A-A and B-B cis compartment interactions in QuiKO mMSCs and Cal27 H3K36M-OE. c Violin plots showing a shift of compartment scores towards 0, indicating a decrease in compartmentalization in QuiKO mMSCs (n = 24832) and Cal27 H3K36M-OE (n = 27148) cells. Boxes represent the 66% quantile interval (from the 17th to 83rd percentiles), with the central point indicating the median. Whiskers extend to the 95% quantile interval (from the 2.5th to 97.5th percentiles). d Hi-C heatmaps illustrating a reduction of nuclear compartmentalization in H3K36M-OE Cal27 cells. e Barplots illustrating a shift of A to B compartments in QuiKO mMSCs and Cal27 H3K36M-OE cells. f-g Representative immunofluorescence images, depicting a reduction of H3K9me3 foci, especially those at the periphery, in mMSC QuiKO and Cal27 H3K36M-OE cells. Nuclei were stained with anti-H3K9me3 antibody and DAPI respectively. h Boxplots showing reduced foci per nuclei in QuiKO mMSCs and Cal27 H3K36M-OE cells. i Boxplots of the average distance of foci to the center of each nucleus, showing that the foci in respective parental cells are further away from the center than in the QuiKO mMSCs or Cal27 H3K36M-OE cells. For a and d, the blue (x-axis) and maroon (y-axis) tracks correspond to MS-normalized H3K9me3 for PA and QuiKO/H3K36M-OE cells, respectively. The 1st eigenvalue is shown, with positive and negative eigenvalues values corresponding to active A (green) and inactive B compartments (red), respectively. In h and i, n = 130 nuclei per condition were sampled for mMSC whereas n = 103 nuclei for Cal27. *** represents p-value < 0.001 and **** represents p-value < 0.0001 from a two-sided Wilcoxon rank-sum test. In h, the p-value for mMSC is 1.7e-24; in Cal27 p = 1.9e-04. In i, the p-value for mMSC is 3.9e-09; in Cal27 p = 5.3e-08. Boxes span the first quartile and third quartile, median is indicated with a center line, and whiskers extend to 1.5 times the interquartile range. Source data are provided as a Source Data file.
