BET inhibition disrupts transcription but retains enhancer-promoter contact

Abstract

In higher eukaryotes, enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes. 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. The formation of phase condensates is thought to be an essential component of enhancer function. Here, we show that pharmacological targeting of cells with inhibitors of BET (Bromodomain and Extra-Terminal domain) proteins can have a strong impact on transcription but very little impact on enhancer-promoter interactions. Treatment with 1,6-hexanediol, which dissolves phase condensate structures and reduces BET and Mediator protein binding at enhancers, can also have a strong effect on gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancerpromoter interactions are separable events. Our findings further suggest that enhancer-promoter interactions are not dependent on high levels of BRD4 (Bromodomain-containing protein 4) and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and loop extrusion by CTCF/cohesin.

Transcription factors: building hubs in the 3D space

“…For example, it has been shown that inhibition of BRD4 [ 87 ] binding or general perturbation of protein condensation by 1,6-hexanediol [ 91 ] treatment result in dissolution of large Med1, BRD4, and PolII condensates in mouse PSCs, preferential loss of SE activity and downregulation of many associated genes. Interestingly, some recent studies demonstrated that although these treatments have drastic effects on enhancer activity and gene expression, they do not affect 3D chromatin organization and enhancer–promoter contacts [ 95 ], arguing against the role of BRD4 and/or protein condensation in long-range interactions. Similarly, inhibition of transcription per se seems to have very little impact on promoter–enhancer contacts [ 95 , 96 ].…”

“…Interestingly, some recent studies demonstrated that although these treatments have drastic effects on enhancer activity and gene expression, they do not affect 3D chromatin organization and enhancer–promoter contacts [ 95 ], arguing against the role of BRD4 and/or protein condensation in long-range interactions. Similarly, inhibition of transcription per se seems to have very little impact on promoter–enhancer contacts [ 95 , 96 ]. These data together argue that the transcriptional activity of a gene and the physical interaction with enhancer(s) are separable events.…”

Revisiting 3D chromatin architecture in cancer development and progression

“…Although strong evidence has revealed that proximity of enhancers and promoters may be a driver of transcription, in some cases, enhancer–promoter interaction alone might not be sufficient to drive transcription. In a recent study performing Capture-C approach at over 60 loci to test the impact of BET inhibitors on enhancer–promoter interactions and transcriptional change in an acute lymphoblastic leukemia cell line, the authors found that BET inhibition has a strong effect on transcription but enhancer–promoter interactions remained undisrupted ( 48 ). In addition, upon glucocorticoid treatment, glucocorticoid receptor (GR) did not reorganize chromatin looping but bound on the sites with pre-established enhancer–promoter interactions and modulated gene transcription ( 49 ).…”

Phenotypic analysis of an MLL-AF4 gene regulatory network reveals indirect CASP9 repression as a mode of inducing apoptosis resistance

“…For the DOT1L model we used nascent RNA-seq of SEM cells treated for 7 days with the DOT1L inhibitor (DOT1Li) EPZ-5676 (38,83), along with H3K79me3 ChIP-seq (38) as a proxy for DOT1L binding (Supplementary Figure S1B). The BRD4 network made use of published nascent RNA-seq of SEM cells treated with IBET-151 for 1.5 hours to inhibit BRD4 binding to chromatin (67) and BRD4 ChIP-seq (60) (Supplementary Figure S1C). We found that, while many of the MLL-AF4 GRN nodes are affected by IBET and DOT1Li treatment, not all of the most central nodes are impacted (Supplementary Figure S1D).…”