BET inhibition disrupts transcription but retains enhancer-promoter contact

Nicholas T Crump,Erica Ballabio,Thomas A Milne,Laura Godfrey,Emmanouela Repapi,Ross Thorne,James O J Davies,Panagis Filippakopoulos,Peng Hua,Christoffer Lagerholm,Jon Kerry,Marta Tapia

doi:10.1038/s41467-020-20400-z

Abstract

Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Bromodomain and Extra-Terminal domain (BET) and Mediator proteins have been shown capable of forming phase condensates and are thought to be essential for super-enhancer function. Here, we show that targeting of cells with inhibitors of BET proteins or pharmacological degradation of BET protein Bromodomain-containing protein 4 (BRD4) has a strong impact on transcription but very little impact on enhancer-promoter interactions. Dissolving phase condensates reduces BRD4 and Mediator binding at enhancers and can also strongly affect gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancer-promoter interactions are separable events. Our findings further indicate that enhancer-promoter interactions are not dependent on high levels of BRD4 and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and, at some sites, CTCF and cohesin.

Highlights

Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes
While chromatin looping mediated by cohesin and bounded by CTCF binding is the most common explanation for controlling large-scale chromatin structure, less is known about what stabilizes more localized enhancer–promoter contacts
We find that reduction of Bromodomain-containing protein 4 (BRD4) and Mediator binding at enhancers has a dramatic and rapid effect on gene expression, but enhancer–promoter looping structures remain stably intact

Summary

Introduction

Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes It is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Emerging work suggests that enhancers function within larger domains, the boundaries of which are defined by the combined effects of CTCF-marked boundary regions and cohesin looping, through a process known as loop extrusion[9,10] It is not entirely clear how these higher-order structures impact enhancer function, but generally speaking functional enhancer–promoter interactions are limited to genes within or at the edges of domains.

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