Fig. 1: The global potential significant impact of crosslinking conditions on DNA ligation preferences.

a The schematic representation of the experimental design employed in this study. b Boxplots showing normalized enzyme cutting frequencies of fragments in open (ATAC-seq peaks, 117855 fragments in total) and closed (H3K27me3 peaks, 116991 fragments in total) regions for libraries crosslinked with varying temperatures and FA concentrations in K562 cells. A Mann-Whitney test was conducted for significant detection with ns (\(p > 0.1\)), * (\(0.01 < p\le 0.1\)), ** (\(0.001 < p\le 0.01\)), and *** (\(p\le 0.001\)). c The proportions of sequencing product types under each crosslinking condition in K562 cells, including dangling ends, self-circles, religations, and valid pairs, which represent sequencing reads with no ligation, ligation between two ends of a single fragment, ligation between adjacent ends in neighboring fragments, and ligation between non-adjacent fragments, respectively. Biological replicates are displayed side by side, with self-circles constituting no more than 0.1% in each library. d The distributions of the four ligation directions in each library for K562 cells. e The proportions of short-range, long-range, and trans interactions among valid interaction pairs in each library for K562 cells. f The contact frequency decay curves for each crosslinking condition in K562 cells.