Coordination of widespread transcription at enhancers and target genes through BRD4 (ChIP-Rx)

Gene transcription by RNA polymerase II (Pol II) is under the control of promoters and distal regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II which correlates 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 transcriptional enhancers in human cells. An integrated multi-omics analysis shows that transcription at most enhancers depends on the BET protein BRD4. We provide evidence for a direct BRD4-mediated coupling of Pol II transcription at enhancers and target genes. Specifically, BRD4 links elongation activation at enhancers and genes by maintaining their proximity. These studies reveal that transcription at enhancers and target genes is coordinated at the level of elongation. Pol II occupancy profiling using standard NET-seq or HiS-NET-seq data for K562 WT cells and upon BRD4-specific degradation in K562 dTAG-BRD4 cells.

RNA聚合酶II（Pol II）介导的基因转录，受启动子与被称为增强子（enhancer）的远端调控元件的调控。增强子本身可被Pol II转录，且其转录水平与其活性密切相关。增强子转录的调控机制，以及其与靶基因转录的协同方式，至今仍未明确。本研究开发了一种高灵敏度的新生延伸转录本测序方法，命名为HiS-NET-seq，以实现对转录过程的高分辨率全景解析，尤其针对增强子这类低转录水平的区域。借助HiS-NET-seq，本研究在人类细胞中发现了全新的转录增强子。整合多组学分析结果显示，绝大多数增强子的转录依赖于BET蛋白（BET protein）BRD4。本研究提供证据表明，BRD4可直接介导增强子与靶基因处的Pol II转录偶联。具体而言，BRD4通过维持增强子与靶基因之间的空间邻近性，实现两者延伸激活过程的连接。本研究揭示，增强子与靶基因的转录可在延伸层面实现协同调控。本研究使用K562野生型（WT）细胞、经BRD4特异性降解处理的K562 dTAG-BRD4细胞的标准NET-seq或HiS-NET-seq数据，开展Pol II占用谱分析。