Abstract

Enhancers are key gene regulatory elements in the non-coding genome that coordinate spatiotemporal gene expression programmes during development, often over large genomic distances. How remote enhancers relay regulatory information to their target promoters has been described as one of the ‘central mysteries of genome function and organisation’. Despite their crucial importance for normal development, only relatively few enhancers have been studied in molecular detail, and their target genes are largely unknown. I will present methodology that we have developed to identify target genes of enhancers genome-wide at high resolution, and I will talk about the insights we have gained from applying this methodology to a range of biological systems and questions. Further, I will present our unpublished work on a novel class of non-canonical enhancers that we have recently discovered in human induced pluripotent stem cells, challenging the current view that enhancers can be identified solely on the basis of a unifying chromatin signature.