Center for dynamic RNA epitranscriptomes - Renewal

动态 RNA 表观转录组中心 - 更新

• 批准号: 10434878
• 负责人: CHUAN HE
• 金额: $ 250万
• 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 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10434878
• 关键词: Adenosine; Affect; Animal Model; Area; Basic Science; Binding Sites; Biological; Biological Process; Biology; Cell Differentiation process; Chemicals; Chemistry; Chromatin; Chromosomes; Clinical; Communities; Complex; Databases; Development; Disease; Engineering; Enhancers; Enzymes; Evolution; Gene Expression Regulation; Genetic Transcription; Genomics; Introns; Investigation; Life; Mammals; Maps; Medical; Messenger RNA; Methods; Methylation; Modification; Mutation; Neurons; Nucleic Acids; Physiological; Play; Post-Transcriptional RNA Processing; Property; Proteins; Protocols documentation; Pseudouridine; RNA; RNA Processing; RNA metabolism; RNA-Binding Proteins; Reader; Regulation; Research; Resolution; Reverse Transcription; Ribosomal RNA; Role; Sampling; Site; Study models; System; Testing; Tissues; Transcript; Transfer RNA; Translations; Untranslated RNA; Up-Regulation; Work; base; bioinformatics tool; chemical group; computational pipelines; demethylation; epitranscriptome; epitranscriptomics; experimental study; human disease; method development; nanopore; new technology; promoter; sequencing platform; stem cell differentiation; transcriptome; Adenosine; Affect; Animal Model; Area; Basic Science; Binding Sites; Biological; Biological Process; Biology; Cell Differentiation process; Chemicals; Chemistry; Chromatin; Chromosomes; Clinical; Communities; Complex; Databases; Development; Disease; Engineering; Enhancers; Enzymes; Evolution; Gene Expression Regulation; Genetic Transcription; Genomics; Introns; Investigation; Life; Mammals; Maps; Medical; Messenger RNA; Methods; Methylation; Modification; Mutation; Neurons; Nucleic Acids; Physiological; Play; Post-Transcriptional RNA Processing; Property; Proteins; Protocols documentation; Pseudouridine; RNA; RNA Processing; RNA metabolism; RNA-Binding Proteins; Reader; Regulation; Research; Resolution; Reverse Transcription; Ribosomal RNA; Role; Sampling; Site; Study models; System; Testing; Tissues; Transcript; Transfer RNA; Translations; Untranslated RNA; Up-Regulation; Work; base; bioinformatics tool; chemical group; computational pipelines; demethylation; epitranscriptome; epitranscriptomics; experimental study; human disease; method development; nanopore; new technology; promoter; sequencing platform; stem cell differentiation; transcriptome

Project Summary/Abstract Chemical modifications on mammalian messenger RNA (mRNA) have recently been shown to play critical and diverse regulatory roles in mRNA metabolism and translation. For example, the most abundant mRNA modification, N6-methyladenosine (m6A), is crucial for mammalian stem cell differentiation and tissue development in almost all systems tested so far. Dedicated proteins, many of which are essential in mammals, have evolved to install, recognize, and remove m6A marks (writers, readers, and erasers, respectively). Dysregulation of m6A methylation has been connected to a variety of human diseases and disorders. Functional roles have also been proposed for other internal modifications present in mammalian mRNA, including, but not limited to: pseudouridine (Ψ), 5-methylcytosine (m5C), 2’-O-methylation (Nm), N1-methyladenosine (m1A), N7- methylguanosine (m7G), and N3-methylcytosine (m3C). Our most recent research has uncovered modifications on chromosome-associated regulatory RNAs (carRNAs), such as promoter-associated RNA (paRNA), enhancer RNA (eRNA), and repeat RNAs, as well as frequent modifications in introns of pre-mRNA. The carRNA modifications have been shown to regulate chromatin state and transcription, and intron modifications may affect pre-mRNA processing. Despite rapid advances in the discovery and functional characterization of various RNA modifications and their effector proteins, a significant bottleneck limits the entire field of epitranscriptomics research: a dearth of quantitative sequencing methods that can comprehensively map most RNA modifications at base resolution with exact modification fraction information. The availability of such methods is critical for assessing the importance of these modifications in different regions of mRNA, examining the effects of dynamic changes in modification fraction, assigning modifications to different writers and analyzing their functional relevance, identifying target transcripts and sites of demethylation and analyzing their functional relevance, discovering new effectors for RNA modifications by overlapping with known RBP-binding sites or genomics features, and evaluating the physiological consequences of RNA modifications in biological processes. We have established both nucleic acid chemistry and directed protein evolution platforms to invent new technologies that transform RNA modifications to be read out as mutations or deletions that are universally compatible with extant sequencing platforms. Computational pipelines and RNA modification databases will be built to support the new method development and epitranscriptome research in the broad community. These new technologies will be optimized to work on low-input samples, particularly neuronal and clinical samples. We will focus on integrating new methods into robust protocols to map multiple RNA modifications in single experiments. Our proposed research will deliver high-throughput, high-resolution, and high-sensitivity methods that simultaneously map multiple RNA modifications in all biological areas.

项目摘要/摘要 最近已证明对哺乳动物信使RNA（mRNA）进行化学修饰，并且 潜水员在mRNA代谢和翻译中的调节作用。例如，最丰富的mRNA 修饰，N6-甲基腺苷（M6A），对于哺乳动物干细胞分化和组织至关重要 到目前为止，几乎所有测试的系统的开发。专用蛋白质，其中许多在哺乳动物中至关重要， 已经演变成安装，识别和删除M6A标记（分别是作家，读者和橡皮擦）。 M6A甲基化失调已与多种人类疾病和疾病有关。功能 还提出了针对哺乳动物mRNA中存在的其他内部修饰的角色，包括但不包括 限制为：伪氨酸（ψ），5-甲基霉素（M5C），2'-O-甲基化（NM），N1-甲基二苯胺（M1A），N7-- 甲基鸟苷（M7G）和N3-甲基霉素（M3C）。我们最近的研究发现了修改 在与染色体相关的调节RNA（CARRNA）上，例如与启动子相关的RNA（PARNA），增强子 RNA（ERNA）和重复RNA，以及前MRNA内含子的经常修饰。 Carrna 已经证明修饰可以调节染色质状态和转录，并且内含子修饰可能会影响 前MRNA处理。尽管在发现和功能表征各种RNA方面取得了迅速的进步 修饰及其效应蛋白，一种显着的瓶颈限制了整个上皮分类组学领域 研究：可以全面绘制大多数RNA修改的定量测序方法的死亡 在基本分辨率下，具有精确的修改分数信息。这种方法的可用性对于 评估这些修饰在mRNA的不同区域的重要性，检查动态的影响 修改分数的变化，为不同作者分配修改并分析其功能 相关性，识别脱甲基化的目标成绩单和位点，并分析其功能相关性， 通过与已知的RBP结合位点或基因组学重叠来发现RNA修饰的新效果 特征，并评估生物过程中RNA修饰的物理后果。我们有 建立了核酸化学和定向蛋白演化平台，以发明新技术 转换RNA修改以读取为普遍兼容的突变或缺失 测序平台。将构建计算管道和RNA修改数据库以支持新的 广泛社区的方法开发和表面参考组研究。这些新技术将是 优化可用于低输入样品，尤其是神经元和临床样品。我们将专注于整合 在鲁棒协议中的新方法，以在单个实验中绘制多个RNA修改。我们提出的 研究将提供高通量，高分辨率和高敏性方法，这些方法仅绘制 在所有生物区域中进行多个RNA修饰。