Biochemical analysis of enhancer–promoter communication in chromatin

Regulation of many biological processes often occurs by DNA sequences positioned over a large distance from the site of action. Such sequences, capable of activating transcription over a distance, are termed enhancers. Several experimental approaches for analysis of the mechanisms of communication over a distance between DNA regions positioned on the same molecule and, in particular, for analysis of enhancer–promoter communication were developed recently. Most of these methods are technically complicated and not applicable for studies of various important aspects of distant interactions in chromatin. As an alternative, we propose a more efficient and versatile method for the study of enhancer–promoter communication in chromatin using a prokaryotic model enhancer–promoter system that recapitulates most of the key aspects of eukaryotic transcriptional enhancer action (including action over a large distance) both in vivo and in vitro. Below we describe the application of this highly efficient experimental system to analyze the structural and dynamic properties of chromatin that allow communication between DNA regulatory regions over a distance.