Fig. 2: Radial chromatin positions and their cell-to-cell variability.
From: Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
a, RAD profiles for a 30-Mb region in chromosome 2. The black line shows the average radial position over the population of structures, and green lines show the radial positions in two different single structures. Arrows depict regions with high cell-to-cell variability. b, Chromatin RAD (top) and δRAD (bottom) in chromosome 2. Subcompartments are color-coded. c, RAD violin plots for each subcompartment. White circles and black bars show the median and the interquartile range (IQR: Q3–Q1). Whiskers show minima and maxima. Q1 and Q3 are the lower and upper quartile of the distribution. Numbers of regions used in each violin plot are: A1: 1,858, A2: 2,723, B1: 1,581, B2: 2,008, B3: 4,187. d, Scatter plots of δRAD versus RAD for chromatin in the A (left) and B (right) compartments. Dashed lines separate low (A-LV and B-LV) and high (A-HV and B-HV) levels of variability. e, Fold-change enrichment of TSA-seq13 and pA-DamID35 signals (left), LADs61 (middle), and replication phases58 (right) for A-LV, A-HV, B-LV, and B-HV. cLAD, constitutive LAD; fLAD, facultative LAD; ciLAD, constitutive inter-LAD; fiLAD, facultative inter-LAD. f, Box plots of the nascent RNA expression levels63 for A-LV and A-HV (Mann–Whitney–Wilcoxon test, two-sided). Numbers of regions used in each box plot are: A-LV: 3,164, A-HV: 2,731. g, δRAD box plots for chromatin with highest and lowest 10% transcript counts37 (Mann–Whitney–Wilcoxon test, two-sided). Numbers of regions used in each box plot are: Top 10%: 686, Bottom 10%: 684. In f and g, the box and the middle line in the box show the the interquartile range (IQR = Q3–Q1) and the median. The vertical lines outside the box extend to a maximum of 1.5 × IQR. h, Distributions for A-LV and A-HV RAD (left) and RAD for three representative A regions with high δRAD (right). The black lines in the left panels indicate the average distribution, and gray areas show the s.d. i, Fold-change enrichment of histone marks in A-LV and A-HV. j, Scatter plots of δRAD versus RAD for A (left) and B (right) chromatin. Top and right panels show RAD and δRAD distributions. k, Fold-change enrichment of subcompartments in A-LV, A-HV, B-LV, and B-HV.
