U2AF2

U2小核核糖核蛋白(snRNP)对pre-mRNA分支位点(BS)的选择对于剪接前体 (A complex)的组装至关重要。RNA解旋酶PRP5校对BS选择，但其潜在机制尚不清楚。2024年1月9日，西湖大学施一公及中国科学技术大学张晓峰共同通讯在Nature Structural & Molecular Biology 在线发表题为“Structural insights into branch site proofreading by human spliceosome”的研究论文，该研究报告了导致前质体组装的两个顺序复合物的原子结构:人类17S U2 snRNP和跨外显子pre-A复合物。PRP5主要通过酸性环占领SF3B1的RNA通路锚定在17S U2 snRNP上；PRP5的解旋酶结构域与U2 snRNA结合；U2 snRNA与BS相互作用的茎环(BSL)被TAT-SF1屏蔽，无法与BS接合。在pre-A配合物中，形成初始的U2-BS双相;PRP5的易位解旋酶结构域停留在U2 snRNA上，酸性环仍然占据RNA路径。pre-A构象被剪接因子SF1、DNAJC8和SF3A2特别稳定。癌症衍生的SF3B1突变破坏了其与PRP5的关联，损害了BS校对。总之，这些发现揭示了PRP5对剪接前体组装和BS选择或校对的关键见解。另外，2024年1月2日，上海科技大学刘如娟、西湖大学施一公及圣裘德儿童医院Xu Beisi等团队合作在Nucleic Acids Research 在线发表题为“THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration ”的研究论文，该研究发现一种RNA修饰-N2 -甲基鸟苷(m2G)沉积在U6 snRNA的G72上(剪接体的催化中心)，促进了人类细胞中有效的pre-mRNA剪接活性。这种修饰在脊椎动物中被证实是保守的。通过明确识别U6特异性序列和结构元件，THUMPD2被证明是负责U6 m2G72的甲基转移酶。敲除THUMPD2消除了U6 m2G72，破坏了pre-mRNA剪接活性，导致人类细胞中内源性pre-mRNA的数千个可选剪接事件发生变化。值得注意的是，异常剪接的pre-mRNA群体引发了无义介导的mRNA衰变途径。进一步表明，THUMPD2与年龄相关性黄斑变性和视网膜功能有关。因此，该研究证明了主要剪接体的RNA表观遗传修饰如何调节全局前mRNA剪接并影响生理和疾病。Pre-mRNA的剪接由剪接体执行，这是一种动态的超分子机器。剪接体通过识别内含子的保守元件:5 ' -剪接位点(5 'SS)、BS、聚嘧啶束(PPT)和3 ' -剪接位点(3 'SS)，组装在pre-mRNA上。首先，U1 snRNP、SF1、U2AF2和U2AF1分别识别5'SS、BS、PPT和3'SS，形成E complex。然后，U2 snRNP取代SF1，使U2 snRNA与BS之间形成双工，从而形成A complex。在高等真核生物中，大多数基因通过选择不同的剪接位点进行选择性剪接。因此，选择BS的A complex的形成是剪接调节的焦点。遗憾的是，人们对E-to-A转换背后的步骤知之甚少。RNA解旋酶PRP5(也称为DDX46)在A complex的组装过程中起关键作用。在人类17S U2 snRNP中，U2 snRNA无法与BS配对，因为U2 snRNA的相关序列形成双链BSL。ATP被PRP5水解导致BSL解绕，从而促进U2-BS双相的形成。在酵母中，Prp5可能校对U2-BS双工，因为Prp5突变允许使用隐性BS和3'SS。然而，PRP5调控剪接保真度的机制尚不清楚。17S人U2 snRNP和人pre-A剪接体的冷冻电镜结构（图源自Nature Structural & Molecular Biology ）大多数已知的癌症衍生的RNA剪接失调突变影响SF3B1的HEAT重复序列中的残基。这些突变大部分聚集在SF3B1的RNA通路上。Hsh155基因中的部分相应突变改变了Prp5相互作用和BS选择。尽管有这些诱人的线索，但这些癌症突变如何干扰正常剪接仍然是一个谜。该研究报道了人类17S U2 snRNP的高分辨率冷冻电镜(cryo-EM)结构和剪接抑制剂捕获的交叉外显子pre-A complex。结合结构导向的生化分析，该研究提出了一个校对BS选择和A complex组装的工作模型。总的来说，该研究为理解剪接体的早期组装过程以及分支位点的识别和选择机制提供了重要的结构信息，同时也为与癌症相关的SF3B1突变的致病机制提供了新的见解。参考文献：Zhang X, Zhan X, Bian T, Yang F, et al. Structural insights into branch site proofreading by human spliceosome. Nat Struct Mol Biol. 2024 Jan 9. doi: 10.1038/s41594-023-01188-0. Epub ahead of print. PMID: 38196034.责编|探索君排版|探索君文章来源|“iNature”End往期精选围观王晓红教授团队：绘制单次冷冻囊胚移植成功的女性植入期外周血microRNA动态表达谱，开拓领域创新研究热文维生素B12在细胞重编程与组织再生中发挥关键作用！热文不孕症治疗新方向！又一导致女性不孕的关键因素被发现热文Let-7家族miRNA或为癌症潜在免疫治疗靶点热文一项最新发现或可用于阿尔茨海默病药物开发点击“阅读原文”，了解更多~

Researchers have identified how three novel genes cause neurodevelopmental disorders. Researchers now have a better sense of the genes' roles in human brain development and function and their ability to serve as potential therapeutic targets in the future. An international study group led by researchers of Children's Hospital of Philadelphia (CHOP) have identified how three novel genes cause neurodevelopmental disorders. Researchers now have a better sense of the genes' roles in human brain development and function and their ability to serve as potential therapeutic targets in the future. The findings were recently published online by the Journal of Clinical Investigation. Over the last couple of decades, researchers have identified more than 1500 genes in different signaling pathways associated with neurodevelopmental disorders. On average, about one third of patients with neurodevelopmental disorders receive a genetic diagnosis. However, little is known about how these genes are networked and how their malfunction leads to these disorders. Prior research in other disorders has shown that issues related to gene splicing may be to blame. Before being turned into proteins, genes are transcribed into introns, or strands of RNA that do not code for proteins, and exons that code for proteins. Introns are removed in a process called splicing, which is carried out by a protein complex called the spliceosome. Variants impacting the spliceosome have rarely been implicated with neurodevelopmental disorders. However, through a series of complex testing, researchers in this study showed that malfunctions in the spliceosome are responsible for some neurodevelopmental disorders. "Using multiple techniques, including phenotyping, genomic sequencing and modeling in fly and stem cells, we were able to map the genetic architecture of three genes associated with neurodevelopmental disorders, particularly developmental delay, intellectual disability and autism," said Dong Li, Ph.D., a research faculty member in the Center for Applied Genomics and the Division of Human Genetics at CHOP and lead author on the study. "Combining fly and human genetics helped us understand the mechanisms of how variants of these genes affect the machinery of the spliceosome and cause these disorders." In this study, researchers utilized genomic and clinical data from unrelated patients with neurodevelopmental disorders. Among the cohort, 46 patients had missense variants of the gene U2AF2 and six patients had variants of the gene PRPF19. In human stem cell and fly models, the researchers noticed issues with the formation of neurites, or protrusions on neurons that give them their shape, as well as issues with splicing and social deficits in the fly models. Deeper profiling revealed that at third gene, RBFOX1, had missense variants that affected splicing and loss of proper neuron function. These findings were later compared with those of patients in the study, which confirmed that variants in the three genes can lead to neurodevelopmental disorders. "We used fruit flies to study the effects of losing the function of these three genes one at a time and found that two genes independently led to brain structural and functional abnormalities, highlighting the essentiality of these genes in development," said study co-author Yuanquan Song, Ph.D., an associate professor from the Department of Pathology & Laboratory Medicine at CHOP. "Apart from identifying patients with such variants in these genes for the first time, our extended translational modeling study efforts aimed to determine the underlying functions for these variants further elucidated their clinical relevance." "Not only does this study identify three causative genes associated with neurodevelopmental disorders, but it helps us understand how critical pre-mRNA splicing is to the development of the central nervous system," said senior study author Hakon Hakonarson, M.D., Ph.D., director of the Center for Applied Genomics at CHOP.

在机制研究上，该研究提出了两种影响CASE剪接的机制。癌症中癌细胞快速地生长增殖需要更快的转录过程，因此癌症中异常的转录或对剪接产生影响。 中国科学院上海营养与健康研究所王泽峰研究团队在Science Advances上，发表了题为A widespread length dependent Splicing regulation in cancer的研究论文。该研究发现了一种全新的在癌症中长度依赖性的可变剪接调控模式。人类基因组90%以上的基因均需要经历可变剪接，剪接的错误调控会导致多种人类疾病，尤其是癌症。越来越多的证据表明，RNA剪接异常与人类癌症密切相关，广泛的剪接失调是癌症的分子标志之一。因此，系统性的探究癌症中可变剪接异常调控将为癌症治疗提供新思路。　　   该研究分析TCGA数据库中大规模的癌症转录组数据，鉴定出在癌症中剪接异常的外显子，发现了癌症中剪接异常的外显子长度均偏向于更短，且这些短外显子在癌症中更倾向于被跳跃。该研究鉴定出494个癌症相关的短外显子（cancer-associated short exons，CASE）并展开进一步研究。科研人员利用CASE的剪接开发出一个用于癌症预测的随机森林模型，可对癌症样本进行准确的预测，AUC达0.9左右。此外，该研究还提出了一种利用CASE剪接计算risk factor的方法来预测癌症病人的预后，在TCGA数据集及其他独立癌症数据集中均具有较好的预测结果。　　   在机制研究上，该研究提出了两种影响CASE剪接的机制。癌症中癌细胞快速地生长增殖需要更快的转录过程，因此癌症中异常的转录或对剪接产生影响。研究对具有不同转录延伸速度的细胞系中可变剪接的分析发现，短的外显子对速度的变化更为敏感，更易受到转录速度变化的扰动而发生外显子的跳跃。转录对剪接的影响是广泛的、无选择性的，该研究进一步表明特定的短外显子在癌症中发生跳跃是受到剪接因子的调控。通过分析ENCODE数据库中大量RNA结合蛋白（RBP）的相关组学数据，研究建立了RBP对CASE剪接的直接调控网络，并鉴定出多个调控CASE剪接的RBP，包括RBFOX2、AQR、U2AF2、PTBP1等。