Mapping Stage-Specific Enhancer Dynamics During the Specification of Human Trophoblast Lineage

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technique for mapping cis-acting regulatory elements in DNA regions, such as enhancers and promoters, that are associated with specific histone modification marks or bound by transcription factors (TFs). By systematically mapping enhancer landscapes across various cell types or differentiation trajectories, this methodology facilitates the discovery of highly regulated genes specific to certain cell types, as well as the underlying transcriptional and epigenetic regulatory mechanisms that establish cellular identity and function. Particular emphasis has been placed on mapping large clusters of enhancers known as super-enhancers (SEs), which are often associated with cell-type-specific master TFs. Unlike typical enhancers, SEs can help to identify previously unknown key TFs specific to certain cell types. Follow-up studies can systematically validate these master regulators and their mechanisms of action, providing a comprehensive framework for deciphering the regulatory architecture underlying cellular identity. This protocol outlines how to map dynamic changes in enhancer and SE usage during human trophoblast differentiation using human trophoblast stem cells (TSCs) and their subsequent differentiation into more specialized cell types.