Fig. 3: Characterization of the regulators of multi-scale chromatin folding.

a–c, Correlation of log₂fc of short-range inter-TAD distances (defined as spatial distances between genomic regions that are less than 3 Mb apart) between sgNIPBL and sgDDX24 (a), sgMRVI1 (b) or sgZNF114 (c). d, A–B compartment score profile of chr22. e, Matrix of average A–B compartment scores of pairs of TADs. f, Top hits with 3D genome effects (log₂fc of inter-TAD distance upon knockout) significantly correlated with the A–B compartment score matrix. Number of traces analyzed: 50, 42, 124, 54, 213, 43, 103, 87 and 53 (left to right). Correlations were derived from 351 data points. Data are presented as correlation coefficients with 95% confidence intervals as error bars. g–i, Correlation between the average A–B compartment score of the TADs and the log₂fc of inter-TAD distances upon FAM69B (g), ZNF114 (h) or FAM13C (i) knockout. j, Hierarchical clustering of correlation coefficients between the log₂fc matrices of inter-TAD distances for top hits. k,l, Correlation of the log₂fc of inter-TAD distances between sgPCBP1 and sgNR4A1 (k) or between sgFAM69B and sgFOS (l). P values in a–c, f–i and k–l were calculated by two-sided t-test. FDR corrections were applied to f.