Center for dynamic RNA epitranscriptomes

动态RNA表观转录组中心

• 批准号: 9070962
• 负责人: CHUAN HE
• 金额: $ 260万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-27 至 2021-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9070962
• 关键词: Adenosine; Area; Base Sequence; Bioinformatics; Biological; Biology; Cancer cell line; Cell physiology; Cells; Chemicals; Circadian Rhythms; Complex; Cytosine; Data Analyses; Databases; Deamination; Development; Disease; Disease Pathway; Engineering; Enzymes; Exhibits; Fatty Acids; Future; Gene Expression Regulation; Health; High-Throughput Nucleotide Sequencing; Human; Immobilization; Immune Tolerance; Induced Mutation; Investigation; Label; Left; Life; Lipids; Malignant Neoplasms; Maps; Messenger RNA; Methods; Methylation; MicroRNAs; Modification; Neurons; Nucleotides; Patients; Play; Post-Transcriptional RNA Processing; Process; Pseudouridine; RNA; RNA Processing; RNA Sequences; RNA Splicing; RNA-Directed DNA Polymerase; Reader; Reading; Research; Resolution; Reverse Transcription; Ribosomal RNA; Role; Sampling; Small Nuclear RNA; Small Nucleolar RNA; Stem cells; System; Technology; Tissues; Transcript; Transfer RNA; Translations; Untranslated RNA; Uridine; Validation; Vertebral column; base; cell type; embryonic stem cell; human disease; invention; neurodevelopment; neurogenesis; piRNA; public health relevance; stem cell differentiation; success; technology development; tool; tool development

 DESCRIPTION (provided by applicant): RNA modifications are ubiquitous in biology and present in all classes of cellular RNAs including eukaryotic messenger and long non-coding RNA. A large fraction of mammalian mRNA/lncRNA modifications are also known to be reversible, highly dynamic, and occur in cell type and cell state dependent manner. The dynamic RNA epitranscriptomes, those involving N6-methyladenosine (m6A) in particular, are known to regulate many cellular activities including mRNA splicing, export, cytoplasmic localization, stability, translation activity, microRNA processing, immune tolerance, and to impact cellular processes including proliferation, development, circadian rhythm, and embryonic stem cell differentiation. Consider m6A in mRNA/lncRNA as an example, dedicated writers, erasers, and readers exist in human cells to orchestrate an additional layer of complex post-transcriptional gene expression regulation. Emerging new functions of RNA modifications are expected to follow, with significant implications on many aspects of human health and disease. Despite high potentials and promises, current epitranscriptome studies are significantly hampered by the lack of technologies that enable quantitative mapping of any type of mRNA/lncRNA modifications at high resolution and high sensitivity. This proposal will develop new methods that target five abundant mRNA/lncRNA modifications, namely m6A, 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudo uridine (Ψ), and 2'O- methyls (Nm) for high-throughput sequencing at single-base resolution and suitable for low input RNA isolated from just hundreds to thousands of cells. New bioinformatics tools will be developed in order to facilitate data analysis. The general approaches proposed can be broadly applied to sequence RNA modifications in other RNA species including more abundant ribosomal RNA, transfer RNA, snRNA, and snoRNA as well as miRNA and piRNA. We will apply the newly developed methods to obtain base-resolution maps of RNA modifications in order to associate with human diseases, and to proof-of-principle studies in neuro-biology. Our proposed research will establish high-throughput, high-resolution, and high-sensitivity methods for epitranscriptome research in all biological areas.

 描述（由申请人提供）：RNA修饰在生物学中普遍存在，并且存在于所有类别的细胞RNA中，包括真核信使和长非编码RNA。大部分哺乳动物mRNA/lncRNA修饰也已知是可逆的、高度动态的，并且以细胞类型和细胞状态依赖性方式发生。已知动态RNA表转录组，特别是涉及N6-甲基腺苷（m6 A）的那些，调节许多细胞活性，包括mRNA剪接、输出、细胞质定位、稳定性、翻译活性、microRNA加工、免疫耐受，并且影响细胞过程，包括增殖、发育、昼夜节律和胚胎干细胞分化。以mRNA/lncRNA中的m6 A为例，人类细胞中存在专门的写入器、擦除器和读取器，以协调额外一层复杂的转录后基因表达调控。RNA修饰的新功能预计将随之出现，对人类健康和疾病的许多方面产生重大影响。尽管具有很高的潜力和前景，但目前的表位转录组研究受到缺乏能够以高分辨率和高灵敏度定量绘制任何类型的mRNA/lncRNA修饰的技术的严重阻碍。该提案将开发针对五种丰富的mRNA/lncRNA修饰的新方法，即m6 A、5-甲基胞嘧啶（m5 C）、N1-甲基腺苷（m1 A）、假尿苷（Ψ）和2 'O-甲基（Nm），用于单碱基分辨率的高通量测序，适用于从数百至数千个细胞中分离的低输入RNA。将开发新的生物信息学工具，以便利数据分析。所提出的一般方法可以广泛地应用于其他RNA种类中的RNA修饰测序，包括更丰富的核糖体RNA、转移RNA、snRNA和snoRNA以及miRNA和皮尔纳。我们将应用新开发的方法来获得RNA修饰的基本分辨率图，以与人类疾病相关联，并在神经生物学中进行原理验证研究。我们拟议的研究将为所有生物领域的表观转录组研究建立高通量、高分辨率和高灵敏度的方法。