Fig. 1: Structural and functional characteristics of enhancer.

A Pioneer factors bind to and activate closed chromatin by mediating chromatin remodeling, making it accessible for other TFs. In contrast, open chromatin structures do not require this mechanism, as TFs can directly access these open enhancers. Pioneer factors recruit epigenetic modifiers to alter the local chromatin environment (such as histone methylation, acetylation, and DNA methylation), further collaborating with other TFs to activate transcription. The figure illustrates a typical enhancer and SE, with SE enriched in TFs and histone modifications (e.g., histone acetylation), driving the expression of cell identity genes. B Chromatin loop (up) and phase separation (down) model of enhancers. In the chromatin loop model, CTCF and cohesins regulate the 3D structure of chromatin through a loop extrusion mechanism, promoting enhancer-promoter interactions. In the phase separation model, the interaction between enhancers, high-density TFs and chromatin modifications forms liquid-like condensates, further modulating gene expression. C High-throughput detection of enhancer activity of DNA fragments using MRPA and STARR-seq methods. (Created with BioRender.com).