RNA-binding protein WDR43 binds prevalently to open chromatin and promotes gene transcription

The intricate regulation of transcription underlies cellular differentiation and development. However, the general relevance of RNA-binding proteins (RBPs) in polymerase (Pol) II transcription is less understood. Here we revealed that WDR43, a novel chromatin-bound RBP, promotes transcription and is essential for self-renewal of embryonic stem cells (ESCs) and early embryonic development. WDR43 binds to promoter-associated non-coding and nascent RNAs, localizes at thousands of gene promoters and enhancers, and interacts with the Pol II transcription machinery. Recombinant WDR43 directly promotes transcription and the release of elongation factor P-TEFb in vitro. Depletion of WDR43 in ESCs leads to global defects in Pol II pause release and mRNA expression. These results demonstrate that WDR43 maintains high-level expression of pluripotency programs by modulating Pol II activity and transcription elongation. To extend these findings, we demonstrated widespread co-occupancy of open chromatin by multiple RBPs, suggesting an unforeseen role for RBPs in transcription control Overall design: Expression profiling by high throughput sequencing and genome occupancy profiling by high throughput sequencing. chrTAP-seq for WDR43.

转录的精密调控是细胞分化与个体发育的核心基础。然而，RNA结合蛋白（RNA-binding proteins, RBPs）在聚合酶（Pol）II转录过程中的普遍作用仍有待阐明。本研究发现，新型染色质结合型RNA结合蛋白WDR43可促进转录过程，且对胚胎干细胞（embryonic stem cells, ESCs）的自我更新及早期胚胎发育至关重要。WDR43可结合启动子相关非编码RNA与新生RNA，靶向结合数千个基因的启动子与增强子，并与Pol II转录机器发生相互作用。体外实验表明，重组WDR43可直接促进转录及延伸因子P-TEFb的释放。在胚胎干细胞中敲除WDR43会导致全局的Pol II暂停释放缺陷及mRNA表达异常。上述结果证实，WDR43可通过调控Pol II活性与转录延伸，维持多能性程序的高水平表达。为拓展上述研究发现，我们进一步证实多种RNA结合蛋白可广泛共占据开放染色质，这提示RNA结合蛋白在转录调控中存在此前未被发现的重要作用。实验整体设计：通过高通量测序进行表达谱分析与基因组占据谱分析，以及针对WDR43的chrTAP-seq实验。