High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription

Abstract

Gene transcription by RNA polymerase II (Pol II) is under control of promoters and distal regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II correlating with their activity. How enhancer transcription is regulated and coordinated with transcription at target genes has remained unclear. Here, we developed a high-sensitive native elongating transcript sequencing approach, called HiS-NET-seq, to provide an extended high-resolution view on transcription, especially at lowly transcribed regions such as enhancers. HiS-NET-seq uncovers new transcribed enhancers in human cells. A multi-omics analysis shows that genome-wide enhancer transcription depends on the BET family protein BRD4. Specifically, BRD4 co-localizes to enhancer and promoter-proximal gene regions, and is required for elongation activation at enhancers and their genes. BRD4 keeps a set of enhancers and genes in proximity through long-range contacts. From these studies BRD4 emerges as a general regulator of enhancer transcription that may link transcription at enhancers and genes.

The ESCRT protein CHMP5 promotes T cell leukemia by controlling BRD4-p300-dependent transcription

“…Therefore, to gain insight into how CHMP5 promoted transcription of BRD4-dependent T-ALL genes like MYC, we wondered if it instead controlled BRD4 binding at distal enhancers defined by hyperacetylated histone modifications, including H3 lysine 27 acetylation (H3K27ac) 45,46 . Notably, recruitment of BRD4 to these hyperacetylated enhancers and super-enhancers promote Pol II pause release and transcriptional elongation 8,40,47,48 . We performed H3K27ac specific ChIP-seq and found diminished H3K27ac density at the TSS, gene bodies, and TES of active genes in CHMP5-KD T-ALL cells ( Figures 3J, 3K and S3E ).…”

“…Importantly, consistent with their downregulated expression ( Figure S3G ), we found drastically diminished H3K27ac density across these key T-ALL genes, with significant loss of H3K27ac and BRD4 at both typical enhancers and super-enhancers in CHMP5-deficient T-ALL cells ( Figures 3M and S3H ). Thus, CHMP5 promotes H3K27ac that defines enhancer and super-enhancers to which BRD4 binds to facilitate Pol II pause release and transcription 8,40,47,48 . Of note, despite reduced H3K27ac density at TSSs, CHMP5 deficiency did not reduce BRD4 binding at TSS, likely reflecting BRD4 binding to promoter-bound proteins like Pol II.…”