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

Enhancer-promoter communication is known to regulate spatiotemporal dynamics of gene expression. Several methods are available to capture enhancer-promoter interactions, but they either require large amounts of starting materials and are costly, or provide a relative low resolution in chromatin contact maps. Here, we present nicking enzyme-assisted open chromatin interaction capture (NicE-C), a method that leverages nicking enzyme-mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of open chromatin interactions at high resolution, especially enhancer-promoter interactions. Using TNF stimulation and mouse kidney aging as models, we applied NicE-C to reveal characteristics of dynamic enhancer-promoter interactions.

Automated summary

The study introduces a new method called NicE-C, which allows for the detection of open chromatin interactions, particularly enhancer-promoter interactions, at a high resolution, with stability and cost-effectiveness. Using this method, the researchers revealed characteristics of dynamic enhancer-promoter interactions in TNF stimulation and mouse kidney aging models.