Fig. 2: DoD (degree of disorder) of innate immune-related TADs during differentiation and activation.

a Hi-C heatmaps at different resolutions. Strong interactions (marked with arrows) were observed around the MYC gene region after differentiation. b TAD dynamics of THP-1 cells during differentiation and activation. c TAD rearrangement, gene expression, and ATAC-Seq peak around STAT1 during M.tb infection. d Typical example of CC chemokine gene cluster. The putative transcription factor (from ENCODE) were labeled with gray box. e The degree of disorder (DoD) was used to evaluate the organizational order of the chromatin architecture in TADs. f Examples of TADs with high and low DoDs and a schematic showing the DoD calculation approach. The P-value for observing interaction frequency is calculated based on the Poisson process. Interactions with P-value ≤ 0.05 are retained. g Relationship between TAD DoD and average gene expression level (normalized read count). The DoD value higher than median was defined as “High DoD”; lower than the median was defined as “Low DoD”. Box-plot with midline = median, box limits = Q1 (25th percentile)/Q3 (75th percentile), whiskers = minimum and maximum values, points = outliers (>1.5 interquartile range). The sample sizes (n) are labeled in the figure. P-values were calculated by two-side Kolmogorov–Smirnov test. h Correlation between TAD DoD and active chromatin epigenetic profile. The y-axis shows the normalized ChIP-seq peaks per TAD. Box-plot with midline = median, box limits = Q1 (25th percentile)/Q3 (75th percentile), whiskers = minimum and maximum values, points = outliers (>1.5 interquartile range). The sample sizes (n) are labeled in the figure. P-values were calculated by unpaired one-sided t-test. i Correlation between the TAD DoD and A, B compartments. In x-axis, B/A means the TADs which contains both A and B compartments. Box-plot with midline = median, box limits = Q1 (25th percentile)/Q3 (75th percentile), whiskers = minimum and maximum values, points = outliers (>1.5 interquartile range). The sample sizes (n) are labeled in the figure. P-values were calculated by unpaired one-sided t-test. j Compare the ratio of change of DoD value in the process of M.tb infection. k Numbers of up- and downregulated genes in the DoD decreased and increased TADs during M.tb infection.