Fig. 5: Perturb-tracing screen identified hits that regulate the morphological properties of nuclei.

a, log₂fc of nuclear intensity unevenness (measured as coefficient of variation (COV) of nuclear voxel intensities) versus −log₁₀ FDR. b, Nuclear intensity unevenness of control and selected hits. Number of cells analyzed: 17304, 12 and 36 (left to right). c, Heat map of nuclear intensity deviation from mean intensity of representative nuclei from non-targeting control (left column) and hit sgRB1 (right column). Scale bar, 10 μm. d, Voxel intensity distribution of all nuclei from non-targeting control (black curve) and hit sgRB1 (red curve). Dashed lines indicate the standard deviations of the distributions. e, log₂fc of nuclear sphericity versus −log₁₀ FDR. f, Nuclear sphericity of control and selected hits. Number of cells analyzed: 17304, 14 and 64 (left to right). g, Representative nuclei images of non-targeting control (left column) and selected hits that regulate nuclear sphericity, TRIM36 (middle column) and EEPD1 (right column). Scale bar, 10 μm. h, Correlation coefficients (bubble color) and significance of correlations (bubble size) between pairs of 3D genome/nucleome features calculated using all top hits. i, Nuclear sphericity values of siCtrl and siCHD7 A549-Cas9 Cells. Number of cells analyzed: 1,156 (siCtrl) and 1,412 (siCHD7). j, Representative DAPI images of siCtrl and siCHD7 A549-Cas9 cells. k, Nuclear sphericity values of sgCtrl, sgPCBP1 and sgZNF114 A549-Cas9 Cells. Number of cells analyzed: 2,474 (sgCtrl), 1,395 (sgPCBP1) and 1,367 (sgZNF114). l, Simulated chromatin polymer folding conformations and the corresponding bounding envelop sphericity values at different chromatin self-interaction energies (K = 1, 0.4 or 0.1). Lower energy corresponds to weaker chromatin interaction. N = 100 simulated conformations for each energy. P values in b, f, i, k and l were calculated by two-sided Wilcoxon rank-sum test. P values in h were calculated by two-sided t-tests. FDR correction was applied to b, f and h. The boxes cover the 25th to 75th percentiles, the whiskers cover the 10th to 90th percentiles, and the lines in the middle of the boxes represent the median values.