Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3′-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3′-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.

RNA 加工的许多步骤发生在 RNA 聚合酶转录过程中。共转录活动被认为在原核生物中很常见，其中缺乏膜屏障允许混合所有基因表达步骤，从转录到翻译。在过去的十年中，真核生物中转录和 RNA 加工之间出现了非凡的协调水平。在这篇综述中，我们讨论了对真核生物和原核生物共转录基因调控的理解的最新进展，比较了方法和机制，并强调了 RNA 聚合酶如何与作用于新生 RNA 的机制之间的惊人相似之处。检测瞬时转录和RNA加工中间体的RNA测序和成像技术的发展促进了转录与剪接、3'端切割和动态RNA折叠协调的发现，并揭示了加工机器和RNA聚合酶之间的物理接触。这些研究表明，内含子保留在给定的新生转录本中可以防止 3' 末端切割并导致转录通读，这是真核细胞应激反应的标志。我们还讨论了新生 RNA 生物发生和转录之间的协调如何驱动原核生物和真核生物中基因表达的基本方面。