Extended Data Fig. 5: Chromatin compaction and TAD borders.
From: Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
a, Average radius of gyration (RG, that is local decompaction) profile for chromatin in the 40–90 Mb region of chromosome 4. The background is color coded by the subcompartment annotations of chromatin (top). Cell-to-cell variability of RG values (δRG) in the structure population for the same chromatin regions. Negative values indicate regions with low RG variability (bottom). Bars are color coded by the subcompartment annotations of the corresponding chromatin regions. b, RG peak frequencies (that is, the fraction of models showing a RG maximum at a given position) for a 6-Mb region in chromosome 4 (80–86 Mb) (top), and Hi-C contact frequency heatmap for the same region showing TAD borders identified by TopDom79 (bottom). Regions with RG peak frequency maxima are shown with gray dashed lines, and either overlap or are very close to TAD borders identified by TopDom (red dashed lines). c, Two representative structures showing chromatin folding patterns for the same chromatin region in b. TAD identities are shown by color code. d, Averaged RG peak frequencies for loci at TopDom TAD borders (green) compared to randomly selected loci (gray). In around 50% of structures, there is a RG peak in the immediate neighboring region of a TAD border (±200 kb, Mann-Whitney-Wilcoxon test, two-sided, p = 1.47×10−200 compared to random) In ~70% of structures there is a RG peak within a ±400 kb range of a TAD border (Mann-Whitney-Wilcoxon test, two-sided, p = 2.46 × 10−7 compared to random). Data are presented as mean values +/− s.d. Numbers of data points at each distance used for TopDom borders (green): 1,839, for random borders (gray): 2,491.
