Fig. 1 | Nature Communications

Fig. 1

From: Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Fig. 1The alternative text for this image may have been generated using AI.

TAD organization arises from modulation of stochasticity. a Top, region of Hi-C contact matrix of chromosome 2L. The black-dotted line demarcates a TAD and pink and cyan boxes represent the Oligopaint- labeled TAD borders (TB). Chromatin epigenetic state is indicated at the bottom using the color code of panel b. Bottom, representative three-color 3D-SIM image in two orientations. DAPI, TB2, and TB3 are shown in gray, pink, and cyan, respectively. Scale bar = 1 µm for the main image. The inset displays 5× amplification of the selected region. b Oligopaint libraries in chromosomes 2L and 3R employed in this study (TB1-16 at TAD borders and IT17-19 within TADs). Colored boxes display the chromatin type of TADs as defined in Supplementary Fig. 1a, b. Red: active, blue: repressed, and black: inactive. Dotted colored lines indicate the combinations of libraries measured. c 3D distance distributions between TB2–TB2 and TB2–TB3. The mean colocalization resolution, estimated from two-color labeling of a single border (40 nm, vertical blue dashed line). Blue and black solid lines represent Gaussian fittings. The absolute contact probability between libraries was obtained from the integral of the area of the Gaussian fitting (shaded gray) below 120 nm (Supplementary Fig. 1e). N = 161 and 556 for TB2–TB2 and TB2–TB3, respectively, from more than three biological replicates. d Absolute contact probability between consecutive borders vs. genomic distance. Chromatin state of TADs is color coded as defined in panel 1b. Error bars represent SEM. e Normalized Hi-C counts between consecutive TAD borders (circles) and random loci (solid gray line) as a function of genomic distance for S2 and late embryonic cells. Matrix resolution = 10 kb. Two biological replicates for each cell type were performed. f Schematic representation of contact probability between and within TADs (solid colored lines) for late embryo and S2 cells at the chromosomal region shaded in panel b. Sizes of TADs (gray-shaded triangles) are proportional to genomic length (scale bar on top). Chromatin type is indicated at the bottom. The thickness of the lines and color indicate the absolute contact probability. Dotted lines indicate inter-TAD contacts. Early embryo measurements are depicted in Supplementary Fig. 1k. Numbers of cells for each combination are provided in Supplementary Fig. 1f–h

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