Extended Data Fig. 4: Predictions of nuclear body related experimental data using 3D models.
From: Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
a, Fraction of mapped histone mark peaks and number of A1/A2 chromatin regions in experimental13 (top) and predicted SON TSA-seq deciles (bottom). b, Predicted mean speckle distances (SpD) for chromatin in experimental SON TSA-seq deciles13. The box and the middle line show the interquartile range (IQR = Q3–Q1) and the median. The vertical lines and whiskers extend to a maximum of 1.5*IQR. Q1 and Q3 are the lower and upper quartile of the distribution. Number of regions used in each decile boxplot is 1,368. c, Spearman correlations between the experimental13 and predicted SON TSA-seq signals (top) using sequence distances to A1 clusters (red), 3D distances to A1 partitions in random territories (blue), 3D distances to A1 regions in the same chromosome (green), and 3D distances to A1 partitions (black), and chromosome 17 profiles (Spearman correlations: 0.37, 0.30, 0.38, 0.78, respectively, bottom). d, Spearman correlations between experimental13 and predicted SON TSA-seq signals (top) using A1 (black) or A2 (red) partitions, or partitions from chromatin with 10% lowest average radial positions (INT, blue), and chromosome 3 profiles (Spearman correlations: 0.88, 0.89, 0.58, respectively, bottom). e, Cell-to-cell variability of speckle distances (δSpD) from DNA-MERFISH6 and models. Error bars show mean +/− s.d. of predicted δSpD values in each imaged δSpD quartile. Number of regions used in each quartile (left to right): 245, 241, 247, 246. Scatter plots of the experimental and predicted signals (left) and chromosome 7 profiles (right) for (f) LaminB1 TSA-seq13 (Pearson correlation: r = 0.78, p = ~0) and (g) LaminB1 pA-DamID34 (Pearson correlation: r = 0.80, p = ~0). h, Scatter plot of lamina association frequencies (LAF) from DNA-MERFISH6 and models (Pearson correlation: r = 0.64, p = ~0). i, Scatter plot of median trans A/B ratios and LAF for each region predicted from models (Pearson correlation: r = −0.90, p = ~0). j, Comparison of nucleoli association frequencies (NAF) from DNA-MERFISH6 and models (Pearson correlation: r = 0.71, p = ~0).
