DNA damage triggers a complex transcriptional response that involves both activation and repression of gene expression. In this study, we investigated global changes in transcription in response to ionizing irradiation (IR), which induces double-strand breaks in DNA. We used mNET-seq to profile nascent transcripts bound to different phosphorylated forms of the RNA polymerase II (RNA Pol II) C-terminal domain (CTD). We found that IR leads to global transcriptional repression of protein-coding genes, accompanied by an increase in antisense transcripts near promoters, called PROMPTs, transcribed by RNA Pol II phosphorylated on tyrosine 1 (Y1P) residue of the CTD. These Y1P-transcribed PROMPTs are enriched for PRC2 binding sites and associated with RNA Pol II proximal promoter pausing. We show the interaction between Y1P RNA Pol II and PRC2, as well as PRC2 binding to PROMPTs. Inhibition of PROMPTs or depletion of PRC2 leads to loss of transcriptional repression. Our results reveal a novel function of Y1P-dependent PROMPTs in mediating PRC2 recruitment to chromatin and RNA Pol II promoter pausing in response to DNA damage.

中文翻译：

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酪氨酸 1-磷酸化 RNA 聚合酶 II 转录 PROMPT，以促进近端启动子暂停并诱导整体转录抑制以应对 DNA 损伤

DNA 损伤会触发复杂的转录反应，涉及基因表达的激活和抑制。在这项研究中，我们研究了电离辐射 (IR) 引起的转录的整体变化，电离辐射会诱导 DNA 双链断裂。我们使用 mNET-seq 来分析与不同磷酸化形式的 RNA 聚合酶 II (RNA Pol II) C 端结构域 (CTD) 结合的新生转录本。我们发现IR导致蛋白质编码基因的整体转录抑制，同时伴随着启动子附近反义转录本的增加，称为PROMPT，由CTD酪氨酸1（Y1P）残基上磷酸化的RNA Pol II转录。这些 Y1P 转录的 PROMPT 富含 PRC2 结合位点，并与 RNA Pol II 近端启动子暂停相关。我们展示了 Y1P RNA Pol II 和 PRC2 之间的相互作用，以及 PRC2 与 PROMPT 的结合。抑制 PROMPT 或消除 PRC2 会导致转录抑制的丧失。我们的结果揭示了 Y1P 依赖性 PROMPT 在介导 PRC2 募集到染色质和 RNA Pol II 启动子响应 DNA 损伤时暂停的新功能。