Fig. 3: Evaluating the order and stochasticity of single-cell chromatin folding in low degree of disorder (DoD) region.

a, b Illustration of how the TAD degree of disorder (DoD) reflect the order and consistency of chromatin folding in single cells. c Flowchart of the single-cell indexed (sci) DLO Hi-C method. d Present cluster analysis result of sciDLO Hi-C datasets by using two-dimensional scatter plots. e Comparison of average contacts around immune genes (±10 Kb around TSS sites) between Thp1-mono, Thp1-macro, and Thp1-M.tb cells. 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. f Simulation of chromatin three-dimensional conformation of representative Thp1-macro and Thp1-M.tb cells by using PyMOL software (version: 2.3.0). The typical innate immune genes NOD2 and BRD7 were labeled with arrows. g Zoom in and comparison of the spatial location of NOD2 and BRD7 in single-cell Thp1-macro and Thp1-M.tb by using simulated nucleus. NOD2 and BRD7 were marked with arrows. h, i Bulk cell chromatin contact matrix and gene expression level of STAT1 TAD of Thp1-macro and Thp1-M.tb cells. The chromatin interaction hot spot which formed in low DOD TAD were marked by dashed box. Chromatin loop-mediated STAT1 and enhancer interaction were labeled by arrows. j, k Single-cell chromatin contacts around STAT1 gene of Thp1-macro and Thp1-M.tb cells. Individual cells have similar chromatin folding patterns in the low DoD TAD. l, m Calculate DOD MD (mean distance) value by using combined single-cell Hi-C contacts of Thp1-macro and Thp1-M.tb cells. Different colors indicate that the chromatin contacts come from different cells.