Develop new bioinformatics infrastructures and computational tools for epitranscriptomics data

为表观转录组数据开发新的生物信息学基础设施和计算工具

• 批准号: 10633591
• 负责人: Mengjie Chen
• 金额: $ 40.13万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-15 至 2027-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10633591
• 关键词: Achievement; Address; Affect; Affinity; Alleles; Base Pairing; Biological Assay; Biological Process; Biology; Biotechnology; Catalogs; Chemicals; Communities; Complex; Computing Methodologies; DNA; Data; Data Set; Databases; Detection; Development; Dimensions; Disease; Foundations; Gene Expression Regulation; Genetic Transcription; Genomics; Goals; Health; Human; Induced Mutation; Innate Immune Response; Measures; Messenger RNA; Metabolism; Methods; Methylation; Modification; Molecular; Mutation; Nature; Nucleotides; Organism; Pathway interactions; Phase; Phenotype; Post-Transcriptional Regulation; Proteins; Protocols documentation; Publishing; RNA; RNA methylation; RNA-Binding Proteins; Regulation; Regulator Genes; Research; Research Personnel; Resolution; Resources; Role; Single Nucleotide Polymorphism; Specificity; Standardization; Statistical Methods; Statistical Models; Structure; Technology; Tissues; Translations; Variant; base; bioinformatics infrastructure; cell type; computerized tools; epitranscriptome; epitranscriptomics; frontier; genetic information; genomic data; human disease; interest; novel; novel strategies; protein function; rapid growth; success; transcriptome; transcriptomic profiling; user friendly software; web portal; web server

Project Summary Dynamic mRNA modifications, such as the m6A-dependent regulation at the mRNA level, add a critical new dimension to post-transcriptional regulation of gene expression. The rapid development of sequencing technologies has transformed the field of epitranscriptomics studies by resulting in the successful profiling transcriptome-wide RNA modifications under different states and conditions. They hold the promise to reveal regulatory machinery of RNA modifications, which contributes to almost every phase of mRNA metabolism and function, thereby impacting diverse biological processes. How- ever, analytical developments in epitranscriptomics lag far behind the pace of technological discovery, and the bioinformatic infrastructure available for epitranscriptomic studies remains limited. The overar- ching goal of this proposal is to address three most pressing challenges facing profiling and interpreting epitranscriptomics. Specifically, we will achieve the following aims: Aim1. Develop statistical methods for RNA modification detection at single nucleotide resolution. Aim 2. Develop computational meth- ods for cell type-specific methylation analysis. Aim 3. Develop web servers that enable integrating RNA modification with a rich catalog of genomics features. All the methods will be implemented in user-friendly software and disseminated to the scientific community. Successful achievement of all aims will dramatically increase the power of epitranscriptomes analysis, leading to better understand- ing of regulatory mechanisms in RNA modifications and their implications in phenotypes and human diseases.

项目摘要 动态mRNA修饰，例如m6a依赖性调节mRNA水平，添加A 基因表达的转录后调节的关键新维度。快速发展 测序技术已通过导致的，从 在不同的状态和条件下，成功填充了整个转录组的RNA修饰。他们 持有揭示RNA修改的调节机制的承诺，这几乎有助于 mRNA代谢和功能的每个阶段，从而影响潜水员生物学过程。如何- 曾经，上次分类组学的分析发展落后于技术发现的空间， 并且可用于表面参考研究的生物信息学基础设施仍然有限。超级 该提案的理论目标是解决专业结构和解释面临的三个最紧迫的挑战 表面参考。开发统计方法 用于单个核苷酸分辨率下的RNA修饰检测。目标2。开发计算MET- 细胞类型特异性甲基化分析的ODS。目标3。开发启用集成的Web服务器 RNA修饰具有丰富的基因组特征目录。所有方法将在 用户友好的软件，并将其传播到科学社区。成功成就 AIMS将大大提高上皮分析的力量，从而更好地理解 - RNA修饰中的调节机制及其在表型和人类中的影响 疾病。