The size of the transcriptional program of long non-coding RNAs in the mammalian genome has engendered discussions about their biological roles¹, particularly the promoter antisense (PAS) transcripts^2,3. Here we report the development of an assay—referred to as chromatin isolation by RNA–Cas13a complex—to quantitatively detect the distribution of RNA in the genome. The assay revealed that PAS RNAs serve as a key gatekeeper of a broad transcriptional pause release program, based on decommissioning the 7SK small nuclear RNA-dependent inhibitory P-TEFb complex. Induction of PAS RNAs by liganded ERα led to a significant loss of H3K9me3 and the release of basally recruited HP1α and KAP1 on activated target gene promoters. This release was due to PAS RNA-dependent recruitment of H3K9me3 demethylases, which required interactions with a compact stem-loop structure in the PAS RNAs, an apparent feature of similarly regulated PAS RNAs. Activation of the ERα-bound MegaTrans enhancer, which is essential for robust pause release, required the recruitment of phosphorylated KAP1, with its transfer to the cognate promoters permitting 17β-oestradiol-induced pause release and activation of the target gene. This study reveals a mechanism, based on RNA structure, that mediates the function of PAS RNAs in gene regulation.

哺乳动物基因组中长非编码 RNA 转录程序的大小引起了关于其生物学作用的讨论¹，尤其是启动子反义 (PAS) 转录本^2,3. 在这里，我们报告了一种检测方法的发展——称为 RNA-Cas13a 复合物的染色质分离——以定量检测基因组中 RNA 的分布。该分析表明，PAS RNA 是广泛转录暂停释放程序的关键守门人，基于停用 7SK 小核 RNA 依赖性抑制性 P-TEFb 复合物。配体 ERα 对 PAS RNA 的诱导导致 H3K9me3 的显着丧失和活化靶基因启动子上基础募集的 HP1α 和 KAP1 的释放。此版本是由于 PAS RNA 依赖性募集 H3K9me3 去甲基化酶，这需要与 PAS RNA 中紧凑的茎环结构相互作用，这是类似调节的 PAS RNA 的一个明显特征。激活 ERα 结合的 MegaTrans 增强子，这对于稳健的暂停释放至关重要，需要募集磷酸化的 KAP1，并将其转移到同源启动子，从而允许 17β-雌二醇诱导的暂停释放和靶基因的激活。这项研究揭示了一种基于 RNA 结构的机制，该机制介导 PAS RNA 在基因调控中的功能。