Poised enhancer chromosomal conformation analysis in unperturbed and CRISPRa-targeted human pluripotent stem cells by 4C-seq

In contrast, these poised enhancers (PEs) are scarce in naive hPSCs that model pre-implantation epiblast. PEs form abundant chromosomal contacts with developmental genes, but when these contacts emerge, how their formation relates to enhancer poising and their functional significance remains incompletely understood.

In this experiment, we targeted CRISPRa to a candidate PE located between two developmental genes, DLX1 and DLX2, and connected only to DLX1. We found that CRISPRa induced the expression of DLX1, but not DLX2, while 3D chromosomal conformation of the locus remained unchanged, pointing to a role of PE contacts in pre-selecting the target genes for subsequent activation during development.