The function of the RNA methylome in animals

RNA甲基化组在动物中的功能

• 批准号: MR/X024261/1
• 负责人: Alper Akay
• 金额: $ 75.53万
• 依托单位: University of East Anglia
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FX024261%2F1
• 关键词: function; RNA; methylome; animals

RNA modifications control diverse biological processes such as embryonic development, sex determination, nutrient sensing and many others. There are currently more than 150 distinct modifications on RNA. The diversity of RNA modifications alongside the proteins required for their synthesis, removal and recognition poses a significant challenge to understanding their biological role. This project aims to uncover (1) the function of RNA methylations in animal development and (2) how RNA methylations are regulated. Many types of RNA contain a diverse number of RNA modifications. Ribosomal and transfer RNAs are heavily modified. Discoveries of internal RNA modifications on messenger RNAs have further expanded the role RNA modifications play in gene expression regulation. Furthermore, several other non-coding RNAs are modified, such as spliceosomal snRNAs and many small regulatory RNAs. We use genetic and biochemical tools to understand how RNA modifications function during germline development and how diet affects RNA modification levels. We use state-of-the-art technologies, including Nanopore Sequencing and high-resolution mass spectrometry. Regulation of gene expression is crucial in the germline. Germ cells give rise to offspring, and gene expression changes in germ cells can directly affect embryonic development. In many organisms, including nematodes and mammals, gene expression changes in the germ cells can have multi-generational consequences. Our research focuses on how RNA modifications and RNA modifying enzymes regulate gene expression in animal germ cells using the nematode Caenorhabditis elegans as a discovery organism. During C. elegans germline development, germ cells proliferate from mitosis to meiosis and differentiate into oocytes or sperm. Therefore, we can use the C. elegans germline to investigate cell proliferation and differentiation at the same time. We will first characterise the role of RNA methyltransferases in mRNA maturation through the regulation of RNA splicing. mRNA maturation is a complex process that involves cap methylation, splicing of introns and poly-adenylation. Efficient RNA splicing requires orchestrating a large protein complex that contains many non-coding RNAs. In addition to removing introns, nematodes and many other organisms that include many parasitic species use trans-splicing during mRNA maturation. Trans-splicing replaces the 5' end of mRNAs with a non-coding SL-RNA. We will use direct RNA sequencing and biochemical approaches to understand how snRNA modifications regulate splicing processes in germ cells.Next, we will investigate how dietary vitamin B12 can regulate RNA modifications. Vitamin B12 is essential for the methionine cycle, which controls S-adenosylmethionine levels. Bacteria and archaea can synthesise vitamin B12, whereas animals must acquire vitamin B12 through their diet. Using our "vegan diet" system and isotope labelling, we will trace how RNA methylation levels change in the presence and absence of vitamin B12. We will use nanopore RNA sequencing to determine isoform level changes in gene expression in the presence and absence of vitamin B12. We will further expand our analysis to bacteria found in the natural diet of C. elegans. We will determine how C. elegans could sense vitamin B12 at the gene expression level. Our research is crucial because it will advance our understanding of how RNA modifications function during development and enable future research in this area by generating tools and resources. Our research addresses a much-overlooked topic connecting diet to chemical changes on RNA.

RNA修饰控制着多种生物过程，如胚胎发育、性别决定、营养感测等。目前，RNA上有150多种不同的修饰。RNA修饰的多样性及其合成、去除和识别所需的蛋白质对理解其生物学作用构成了重大挑战。本项目旨在揭示（1）RNA甲基化在动物发育中的功能和（2）RNA甲基化是如何调节的。许多类型的RNA含有不同数量的RNA修饰。核糖体和转移RNA被严重修饰。信使RNA内部RNA修饰的发现进一步扩大了RNA修饰在基因表达调控中的作用。此外，其他几种非编码RNA被修饰，如剪接体snRNA和许多小的调控RNA。我们使用遗传和生物化学工具来了解RNA修饰在种系发育过程中的作用以及饮食如何影响RNA修饰水平。我们使用最先进的技术，包括纳米孔测序和高分辨率质谱。基因表达的调控在生殖系中至关重要。生殖细胞产生后代，生殖细胞中基因表达的变化可以直接影响胚胎发育。在许多生物体中，包括线虫和哺乳动物，生殖细胞中的基因表达变化可能会产生多代后果。我们的研究重点是如何RNA修饰和RNA修饰酶调节基因表达的动物生殖细胞使用线虫作为发现生物。在C.在线虫生殖系发育中，生殖细胞从有丝分裂增殖到减数分裂，并分化成卵母细胞或精子。因此，我们可以使用C。elegans胚系，同时研究细胞增殖和分化。我们将首先阐明RNA甲基转移酶通过调节RNA剪接在mRNA成熟中的作用。mRNA成熟是一个复杂的过程，涉及帽甲基化、内含子剪接和多聚腺苷酸化。高效的RNA剪接需要协调包含许多非编码RNA的大型蛋白质复合物。除了去除内含子之外，线虫和包括许多寄生物种的许多其他生物在mRNA成熟期间使用反式剪接。反式剪接用非编码SL-RNA替换mRNA的5'末端。我们将使用直接RNA测序和生物化学方法来了解snRNA修饰如何调节生殖细胞中的剪接过程。接下来，我们将研究膳食维生素B12如何调节RNA修饰。维生素B12对甲硫氨酸循环至关重要，它控制S-腺苷甲硫氨酸水平。细菌和古细菌可以合成维生素B12，而动物必须通过饮食获得维生素B12。使用我们的“纯素饮食”系统和同位素标记，我们将追踪在存在和不存在维生素B12的情况下RNA甲基化水平的变化。我们将使用纳米孔RNA测序来确定在存在和不存在维生素B12的情况下基因表达的亚型水平变化。我们将进一步扩大我们的分析，以发现在自然饮食中的细菌C。优雅的我们将确定C。线虫能在基因表达水平上感受到维生素B12。我们的研究至关重要，因为它将促进我们对RNA修饰在发育过程中如何发挥作用的理解，并通过生成工具和资源来实现该领域的未来研究。我们的研究解决了一个被忽视的话题，将饮食与RNA的化学变化联系起来。