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Fig. 2 | Genome Biology

Fig. 2

From: Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors

Fig. 2

The general correspondence between TF presence and spatial co-localization. a Relating TF binding site occupancy with homotypic Hi-C contacts. Correspondences between mean homotypic occupancy and CCL-score (from Hi-C) for all TFs collectively are shown as regression plots and sub-divided according to promoter or enhancer classes (see the “Methods” section). For comparative purposes, the all-site average is shown in grey in the left panel. Accessible sites for different TFs were rank normalized, combined and grouped into ten bins according to CCL-score. Pearson’s R2 values are shown alongside the percentage change in occupancy change across the CCL range. Error bars indicate standard deviation from resampling. b Relating TF binding site occupancy with heterotypic Hi-C contacts. Similar to a, but considering interactions between different TF types. For a given site of a specific TF, interactions with all other heterotypic sites were considered collectively to define the integrated heterotypic CCL-score (Eq. 5). Data is separated according to whether sites are found in enhancer regions (blue) or promoter regions (red). All TFs were studied collectively by rank normalization of their heterotypic CCL-score. c Occupancy differences between high and low co-localization sites for individual TFs. For each lymphoblastoid TF, the fractional increase in binding site occupancy when comparing the top and bottom terciles of CCL-scores is shown as a bar plot. Stars denote significance level (FDR-adjusted p value for a G-test with Williams’ correction). d Dissecting the homotypic TF occupancy to Hi-C relationship according to strong and weak sequence motifs. As in a, but sub-divided according to promoter or enhancer classes (see the “Methods” section) with either strong (left) or weak (right) DNA sequence motifs, based on motif p values obtained from FIMO motif scans [70]. e Dissecting the homotypic TF occupancy to Hi-C relationship according to promoter expression. As in a, but with gene promoter regions classified according to strength of RNA-seq signal. Accessible sites for different TFs were rank normalized, combined and grouped into ten bins according to CCL-score. Pearson’s R2 values are shown alongside the percentage change in occupancy change across the CCL range. Error bars indicate standard deviation from resampling. f Relating spatial and 1D sequence densities of TF sites in mESC genome structures. The color matrix shows the distribution, for all mESC TFs combined, of the spatial density enrichment (SDE) at different rank-normalized sequence densities. Line plots represent mean values for the distribution of SDE across decile groups of sequential TF density and either represent all TF sites (yellow), enhancers (blue), or promoters (red). Error bars represent standard error of the mean and triangles the 25–75th percentiles. Data shown is for homotypic sites, aggregated for all mESC TFs studied

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