Fig. 4: SON TSA-seq predictions using 3D structures.
From: Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
a, Average GRO-seq signal63 (RPM) of chromatin regions with respect to their 3D distances to partition centers in different Hi-C subcompartments or interior (INT) chromatin (Methods). b, Comparison of average GRO-seq signals63 for chromatin in large (size > Q3, dark colors) and small (size < Q1, light colors) spatial partitions for different subcompartments. Error bars show mean ± s.d. Total numbers of data points (all partitions in all structures) used in statistics are: A1 large: 257,454, A1 small: 245,698, A2 large: 354,618, A2 small: 689,536, B1 large: 212,557, B1 small: 629,112, B2 large: 306,571, B2 small: 364,678, B3 large: 778,382, B3 small: 136,143. c, Average SON TSA-seq signals13 of chromatin regions with respect to their 3D distances to partition centers in Hi-C subcompartments and interior (INT) chromatin (Methods). d, Procedure for SON TSA-seq signal prediction from 3D models: The geometric centers of identified A1 partitions in each single structure are used as point sources for the simulation of SON-TSA-produced tyramide free-radical diffusion13. SON TSA-seq signals are averaged over all structures (Methods). The rightmost image shows a cross-section of the predicted TSA-seq signal density distribution in a genome structure. e, Comparison of the experimental and predicted SON TSA-seq profiles for chromosome 2 (Pearson correlation: r = 0.90, P = ~0). f, Scatter density plot of the experimental versus predicted SON TSA-seq signals genome-wide (Pearson correlation: r = 0.87, P = ~0). g, Scatter density plot of the predicted speckle association frequency (SAF) versus SAF determined in DNA-MERFISH experiments6 for 1,041 imaged loci (Pearson correlation: r = 0.77, P = ~0). h, Scatter density plot of the median trans A/B ratios predicted in our models (Methods) versus those from the DNA-MERFISH experiment6 for 724 imaged loci that share the same compartment in GM12878 and IMR-90 cells (Pearson correlation: r = 0.70, P = ~0). i, Scatter plot of the predicted median trans A/B ratios versus SAF for each chromatin region in our models (Pearson correlation: r = 0.98, P = ~0).
