Nuclear Accumulation of YTHDF1 Regulates mRNA Splicing in the DNA Damage Response
收藏资源简介：
YTH domain-containing family protein 1 (YTHDF1), a reader of N6-methyladenosine, has been implicated in regulating RNA metabolism in the cytosol. Here we report a role of YTHDF1 within the nucleus in response to genotoxic stress. Upon radiation, YTHDF1 is phosphorylated at serine 182 in an ATR-dependent manner. This phosphorylation inhibits exportin 1-mediated nuclear export of YTHDF1, resulting in its accumulation within the nucleus. Nuclear YTHDF1 enhances the binding capacity of SRSF2 to a group of m6A-modified exons, leading to increased exon inclusion. Specifically, YTHDF1 promotes splicing and expression of DNA repair genes, such as BRCA1 and TP53BP1, thereby mitigating excessive DNA damage. Depletion of YTHDF1 sensitizes cancer cells to radiation treatment. Altogether, our study reveals a crucial role of YTHDF1 in m6A-mediated mRNA splicing in the DNA damage response, proposing it as a potential target for radiation therapy. [dataset 1] 3 samples. m6A-IP-seq of polyA+ RNA samples, including m6A input, m6A-IP in HEK293T cell line and RNA-seq in YTHDF1-KO HEK293T cells after X-ray exposure [dataset 2] 2 samples. RNA-Seq samples of SRSF2-CTL and SRSF2-KD HEK293T cells after X-ray exposure; [dataset 3] 1 samples. Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP-seq) for YTHDF1 in HEK293T cell line after X-ray exposure;[dataset 4] 2 samples.RNA Immunoprecipitation (RIP-seq) for SRSF2 in YTHDF1-WT/KO HEK293T cell line after X-ray exposure;
含YTH结构域家族蛋白1（YTHDF1）作为N6-甲基腺嘌呤（N6-methyladenosine）的识别读取蛋白，已被证实可调控细胞质内的RNA代谢过程。本研究首次报道了YTHDF1在细胞核内参与应答基因毒性应激的全新功能。经X射线辐照后，YTHDF1会在丝氨酸182位点发生依赖于ATR的磷酸化修饰；该磷酸化事件可抑制输出蛋白1（exportin 1）介导的YTHDF1核输出，使其在细胞核内发生积累。核内积累的YTHDF1能够增强丝氨酸/精氨酸剪接因子2（SRSF2）与一组携带m6A修饰的外显子的结合能力，进而提升外显子保留率。具体而言，YTHDF1可促进DNA修复基因（如BRCA1与TP53BP1）的剪接与表达，从而减轻细胞内过度的DNA损伤。敲除YTHDF1可使癌细胞对放射治疗更为敏感。综上，本研究揭示了YTHDF1在DNA损伤应答过程中通过m6A介导调控mRNA剪接的关键作用，并提出其可作为放射治疗的潜在靶点。 [数据集1] 共3个样本：针对X射线辐照后的样本开展多聚腺苷酸化RNA（polyA+ RNA）m6A免疫沉淀测序（m6A-IP-seq），涵盖HEK293T细胞系的m6A输入对照、m6A免疫沉淀样本，以及YTHDF1敲除（YTHDF1-KO）HEK293T细胞的RNA测序（RNA-seq）样本； [数据集2] 共2个样本：X射线辐照后SRSF2对照（SRSF2-CTL）与SRSF2敲低（SRSF2-KD）HEK293T细胞的RNA测序样本； [数据集3] 共1个样本：X射线辐照后HEK293T细胞系中YTHDF1的光激活核糖核苷增强交联免疫沉淀测序（PAR-CLIP-seq）； [数据集4] 共2个样本：X射线辐照后YTHDF1野生型（YTHDF1-WT）与敲除型HEK293T细胞系中SRSF2的RNA免疫沉淀测序（RIP-seq）
