New insights into promoter-enhancer communication mechanisms revealed by dynamic single-molecule imaging

Abstract

Establishing cell-type-specific gene expression programs relies on the action of distal enhancers, cis-regulatory elements that can activate target genes over large genomic distances - up to Mega-bases away. How distal enhancers physically relay regulatory information to target promoters has remained a mystery. Here, we review the latest developments and insights into promoter-enhancer communication mechanisms revealed by live-cell, real-time single-molecule imaging approaches.

Keywords: enhancers; genome organization; optical nanoscopy; single-molecule approaches; transcription.

Figure 1. Sub-diffraction clusters of RNA Pol II and RFs at the Pou5f1 transcription site discovered by optical nanoscopy.

Top row: whole nucleus live-cell images, showing the Pou5f1 transcription site (Nascent RNA visualized using MCP-mNeonGreen binding to 24xMS2 stem-loops), as well as RNA Polymerase II (Rpb1 subunit), Sox2, Cdk9, Brd4 and Mediator (Med22 subunit), visualized using SNAP-tag knock-ins and a SiR dye. Bottom row shows zoomed-in regions of the vicinity of the transcription site in live-cells, showing small (5-20 molecules), sub-diffraction clusters of Pol II and RFs. Top row: A.P. and J.L., unpublished data; bottom row: reproduced, with permission, from [44].

Figure 2. Proposed physical models for enhancer-promoter communication.

Dynamic P-E contact model: RFs stay mostly bound to cognate DNA and chromatin sites at the enhancers; RF interactions with the transcription machinery at the promoter are then facilitated by dynamic movements of the chromatin polymer that bring promoter and individual enhancers in molecular proximity. Local RF trapping model: P-E are staying at approximate proximity (100-200nm) while single RF molecules can dissociate from their DNA/chromatin sites and explore the local environment of the clustered enhancers, possibly through constrained motion, searching for the transcription machinery at the promoter.