Fig. 3: Alterations of chromatin structure during differentiation resembled that in Matr3 KO cells, and Matr3 loss opens regulatory chromatin regions specific to differentiation.

a Contact frequency enrichment for compartment A (bottom right) and B (top left) in the differentiated parental cell. The difference between uninduced (Unt) and differentiated (Diff) cells was calculated as the log2 ratio of average interaction intensity (obs/exp) at 50 kb, and shown as a differential map b and the change was further confirmed in Fig. S2b. Results of replicate experiments are shown in Fig. S2d-d’. c Analysis of the significantly altered TADs revealed that most of the TADs during differentiation in compartment A had increased intra-TAD interaction frequency, while those in B had decreased contact frequency. Numbers in the pie chart represent TADs with significantly changed intra-TAD interaction frequency. d Hi-C interaction data binned at 25 kb resolution was aggregated at TAD boundaries and the difference was calculated by log2 ratio of differentiated and uninduced cells. Results of replicate experiments are shown in Fig. S2e-e’. e Average insulation score²⁹ across TAD boundaries increased during differentiation and in Matr3 KO. Results of replicate experiments are shown in Fig. S2f-f’. f Genomic length distribution of Hi-C contacts. Results of replicate experiments are shown in Fig. S2h-h’. g Average TAD size for each chromosome identified using³⁰ across two independent experiments (Unt.Pa vs. Unt.KO: p = 0.007, Unt.Pa vs. Diff.Pa: p = 0.0004, Diff.Pa vs. Diff.KO: p = 0.46, by two-sided Wilcoxon signed-rank test, respectively; Cohen’s d = 0.44, Cohen’s d = 0.84, Cohen’s d = 0.08, respectively). Center lines, boxes, and whiskers represent the median value, first and third quartiles, and 1.5 interquartile range of the samples, respectively. h ATAC-seq peaks unique to Matr3 KO compared to parental cells (gained peaks) were used for motif analysis. The natural logarithm of the p-values calculated using the binomial distribution are shown in the heatmap and in Table S1. i The number of ATAC-seq peaks proximal or distal to TSS was counted. Then, the peaks in the distal region were further analyzed to overlap the ChIP-seq peaks for histones j.