Extended Data Fig. 3: Validation of CHD7 perturbation phenotypes using overexpression.
From: Perturb-tracing enables high-content screening of multi-scale 3D genome regulators
a, A-B compartment profile of chr22 in A549-Cas9 cells with GFP overexpression. b, A-B compartment profile of chr22 in A549-Cas9 cells with CHD7 overexpression. c, Polarization indices of cells with GFP (white) and CHD7 (orange) overexpression and the corresponding randomized controls (shadowed). Number of traces analyzed: 2,701 (GFP and GFP-random) and 1,015 (CHD7 and CHD7-random). d, Compartmental contact frequencies of cells with GFP of CHD7 (shadowed) overexpression in A compartments (red), across A and B compartments (purple) and in B compartments (blue). Number of traces analyzed: 3,157 (GFP OE) and 1,174 (CHD7 OE). e, Log2 fold change of inter-TAD distance of CHD7 overexpression compared to GFP overexpression. Number of traces analyzed: 3,157 (GFP OE) and 1,174 (CHD7 OE). f, Overall inter-TAD distance of chr22 in cells with GFP and CHD7 overexpression. Number of traces analyzed: 3,157 (GFP OE) and 1,174 (CHD7 OE). g, Radii of gyration of chr22 in cells with GFP and CHD7 overexpression. Number of traces analyzed: 2,701 (GFP OE) and 1,015 (CHD7 OE). h, Log2 fold change of short-range and long-range inter-TAD distances between CHD7 and GFP overexpression. Number of traces analyzed: 3,157 (GFP OE) and 1,174 (CHD7 OE). i, Area of chr22 territories per cell measured by whole chromosome paint in cells with GFP and CHD7 overexpression. Number of cells analyzed: 1,715 (GFP OE) and 1,538 (CHD7 OE). P values in c, d, g and i were calculated by two-sided Wilcoxon rank sum test. P values in f and h were calculated by two-sided Wilcoxon signed rank test. 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.
