NicE-C efficiently reveals open chromatin associated chromosome interactions at high resolution

Enhancer-promoter communication is known to regulate spatiotemporal gene expression. Here, we present NicE-C, a method that leverages nicking enzyme mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of chromatin interactions among open chromatin regions (e.g., between enhancers and promoters). Demonstrating its application utility, NicE-C revealed dynamic enhancer-promoter interactions associated with gene expression changes after TNF? stimulation in HeLa cells and during aging process in mice kidney. Overall design: NicE-C are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation, IMR90 cells, Mice kidney of young and old mice. RNA-seq are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation and kidney of young and old mice. HiC and NicE-seq are generated for HeLa cells.