lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [CDK9 ChIP-Seq]

Numerous long noncoding RNAs (lncRNAs) are generated in response to external stimuli, but the scope and functions of such activity are not known. Here, we provide insight into how the transcription of lncRNAs are connected to DNA damage response by identifying a lncRNA ZFAS1, which is required for cell cycle arrest, transcription regulation and DNA repair. Mechanistically, ZFAS1 facilitates the changing hyperphosphorylated forms of the large subunit of RNAPII around transcription initiation sites by directly targeting the regulated genes. We revealed extensive transcription shutdown and concomitant stimulated engagement of RNAPII-Ser2P are crucial for repair and cell survival upon genotoxic stress. Finally, ZFAS1 knockout in mice dampened transcription-coupled nucleotide excision repair (TC-NER) and led to kidney dysplasia. Our study extends the understanding of lncRNAs in DNA damage repair (DDR) and implies a protective role of lncRNA against DDR-deficient developmental disorders. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CDK9 in the WT and ZFAS1-depleted cells with or without UV-C irradiation.

众多长链非编码RNA（long noncoding RNA，lncRNA）可在外界刺激下生成，但这类转录活动的作用范围与生物学功能尚不明确。本研究通过鉴定长链非编码RNA ZFAS1，揭示了长链非编码RNA的转录与DNA损伤应答的关联机制：ZFAS1对于细胞周期阻滞、转录调控及DNA修复均不可或缺。机制层面上，ZFAS1可通过直接靶向受调控基因，介导RNA聚合酶II（RNA polymerase II，RNAPII）大亚基的高度磷酸化形式在转录起始位点附近的动态变化。本研究发现，广泛的转录沉默以及伴随的、受刺激诱导的丝氨酸2位点磷酸化RNA聚合酶II（RNAPII-Ser2P）结合，对于遗传毒性应激下的DNA修复与细胞存活至关重要。最后，在小鼠体内敲除ZFAS1会削弱转录偶联核苷酸切除修复（transcription-coupled nucleotide excision repair，TC-NER），并引发肾脏发育异常。本研究拓展了学界对长链非编码RNA在DNA损伤修复（DNA damage repair，DDR）中作用的认知，并提示长链非编码RNA可对抗DNA损伤修复缺陷相关的发育异常疾病，发挥保护作用。实验整体设计：对野生型（wild type，WT）与ZFAS1敲低细胞，分别施加或不施加UV-C辐照，开展针对CDK9的染色质免疫共沉淀测序（Chromatin immunoprecipitation DNA-sequencing，ChIP-seq）。