Fig. 5: Excessive crosslinking enhances the reliability of chromatin loop detection without significantly impacting its sensitivity.

a The relationship between the number of loops and the number of anchors involved across all crosslinking conditions in K562 cells. Dots without edges represent individual biological replicates, while those with edges represent their merged data. The dashed line and shadow region indicate the fitted linear model of these two numbers and their corresponding confidence intervals. b The heatmap of CTCF, SMC3, H3K4me3, and H3K27ac ChIP-seq signals at loop anchors in each crosslinking condition in K562 cells. Conditions ranging from 37 °C/0.5% FA to 37 °C/2% FA are displayed from left to right in each panel. The BL Hi-C library is placed on the far right. Signals are aligned according to the maximum value in the anchor bins. Average signal profiles among all anchors are shown at the top of each heatmap. In each heatmap, only the top 50% (for CTCF and SMC3) and top 30% (for H3K4me3 and H3K27ac) anchors with the highest average signals are displayed for comparability. c The enrichment of enhancer (E) and promoter (P) involved loops in each crosslinking condition. Colors indicate the observed/expected number of loops, where the expected numbers are calculated using a contingency table assuming independence between enhancer/promoter involvement and crosslinking conditions. d The enrichment of CTCF involved loops in each crosslinking condition. The number of loops with 0, 1, and 2 binding CTCF motifs at occupied anchors is marked. The structure of this panel is identical to (c). e The expression levels of three gene groups classified based on the elements they interact with through loops in each crosslinking condition. The \(p\)-values of Kruskal-Wallis tests measuring the differences between the three groups in each condition are indicated below. Thin and thick horizontal lines mark the mean values of average expression levels among crosslinking conditions for the “trivial loop” and “E/P loop” groups, respectively. On each box plot, the number of genes involved in the corresponding groups (sample sizes) is marked.