Fig. 2: Matr3 loss leads to global reorganization of 3D genome architecture.

a, b The first eigenvector (EV1) indicating the genomic compartment for chromosome (chr) 1 and Hi-C contact matrices at 500 kb resolution. c Representative region (green dashed box in Fig. 2a, b) of Hi-C data at 25 kb resolution with the compartment signal. Arrowheads indicate altered interactions. d Snapshot of Hi-C data at chr 1 (red dashed box in Fig. 2a, b) showing each compartment, compartment difference, and insulation score of parental (green) and Matr3 KO (magenta) cells. Compartment switch is apparent in the indicated regions marked with dashed boxes. One of the altered regions is plotted with Hi-C contact matrices at 25 kb resolution in (e). f Contact frequency enrichment for compartments A (bottom right) and B (top left). Compartmentalization saddle plots were calculated by normalized interaction frequencies between loci of 100 kb bins arranged by their eigenvector values (EV1). The numbers of the heatmaps indicate the average compartment strength quantified by calculating the ratio of homotypic (A-A or B-B) to heterotypic (A-B) compartment interactions of the top 20% sorted EV1 values. The difference was calculated as log2 ratio of average interaction intensity (obs/exp) in Matr3 KO and control at 50 kb, and shown as a differential map g, and the change was further confirmed in Fig. S2a. h Hi-C interaction data binned at 25 kb resolution was aggregated at TAD boundaries and the difference was calculated by log2 ratio of Matr3 KO and parental cells. Results of replicate experiments for f–h are shown in Fig. S1h-h’. i Analysis of the dynamically altered TADs in Matr3 KO revealed that most of the TADs in compartment A had increased intra-TAD interaction frequency, whereas those in B had decreased contact frequency. Numbers in the pie chart represent TADs with significantly changed intra-TAD interaction frequency, which was defined as p < 0.05 and log2 fold change > 0.15 or < -0.15.