Fig. 7: Impact of Matr3 loss on chromosomal architecture extends to embryonic stem (ES) cells.

a 3573 and 3575 differential loops lost in Matr3 KO and during differentiation, respectively, were identified and significantly overlapped (2996, 84%). Random overlap for lost differential loops: 212 (out of 3650), 6%, p = 1e-5 from the permutation test. b, c Interaction pile-up maps of Hi-C data at the boundaries defined by each set of CTCF b and Rad21 c ChIP-seq peaks. The normalized pile-up interaction frequency observed over expected values indicates stronger insulation at regions of parental cells that are maintained (common) than at altered sites (uniq) in Matr3 KO cells. The results were confirmed in 2-3 independent experiments (Fig. S5i-j). Hi-C data of Matr3 KO compared to parental cells at altered sites are shown in Fig. S6a-b’. d ChIP-seq data sets of CTCF in mouse ES cells were quantitatively compared, and the results of independent experiments were combined to generate a more stringent peak list as described above (Fig. S6g). Then, the enrichment of the peaks in each experiment was investigated and confirmed (Fig. S6i). CTCF enriched less strongly at altered sites (uniq) than sites maintained (common) in Matr3 KO cells and during differentiation (diff) (p < 2.2e-16, p < 2.2e-16, respectively, by two-sided t test; Cohen’s d = 1.31, Cohen’s d = 0.97, respectively). In box plots, the centre line represents the median, box limits show upper and lower quartiles, and whiskers extend to 1.5 × interquartile range. The CTCF peak-mapped genes were placed into ventiles (x-axis) from highest to lowest gene scores corresponding to genes with the most significant peak changes. The genes within each ventile were then overlapped with genes whose expression was altered (y-axis) in Matr3 KO compared to parental cells e and during differentiation f. Analysis was performed on both MEL and mouse ES cells and the significance of the association was assessed using the one-sided hypergeometric test (p = 9.5e-08, p = 2.3e-26, respectively in e and p = 6.6e-04, p = 4.4e-14, respectively in f). Fold overlap over random: 1.4503, 1.428, 1.4857, 1.514, respectively.