Specialized Tools and Auto-updatable Scalable Interactive Databases to Study isomiRs, tRFs and rRFs in Human and Mouse

用于研究人类和小鼠 isomiR、tRF 和 rRF 的专用工具和可自动更新、可扩展的交互式数据库

基本信息

批准号：
10736401
负责人：
Isidore Rigoutsos
金额：
$ 55.31万
依托单位：
THOMAS JEFFERSON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-08-02 至 2027-05-31
项目状态：
未结题

项目摘要

This project focuses on three categories of small RNAs: the isoforms of microRNAs (miRNAs) that are known as isomiRs; the fragments that are derived from transfer RNAs (tRNAs) and are known as tRFs; and, the frag- ments that are derived from ribosomal RNAs (rRNAs) and are known as rRFs. IsomiR, tRFs, and rRFs have several important properties that warrant their detailed study: (1) They account for ~80% of all small RNAs in a cell. (2) They regulate the abundance of messenger RNAs (mRNAs) and pro- teins. (3) Their expression patterns depend on cellular “context” (e.g., tissue type, disease type). (4) In hu- mans, their expression patterns additionally depend on “personal attributes” (e.g., sex, genetic ancestry, age). To correctly mine isomiRs, tRFs, and rRFs from RNA-seq data the ideal tools must address several compli- cating factors. First, the same short sequence (e.g., tRF) can arise from different parental RNAs. These parental RNAs can belong to the same sub-type (e.g., different tRNA isodecoders of the same tRNA isoacceptor) or different sub-types (e.g., isodecoders from different tRNA isoacceptors). Second, the sequences of many iso- miRs, tRFs, and rRFs can also be found in unrelated regions of the genome. Third, paralogues and/or incomplete copies of miRNAs, tRNAs, and rRNAs riddle the nuclear genomes of many organisms including human and mouse. The details of these complicating factors are specific to the RNA type and to the genome. Consequently, the ideal tools must be target-genome-specific. The complicating factors and the need for genome specificity appeared in the literature only recently. As a result, most available tools to date have been general-purpose and do not account for these complications. Not surprisingly, most available databases were built using general-purpose tools. Without realizing the underlying shortcomings, many researchers relied on the information provided by these tools and databases to design experiments and analyze their data. In turn, this has led to many published articles that unintentionally describe findings of unclear value about molecules that are not always isomiRs, tRFs, or rRFs. We will address these gaps as follows. In Aim 1, we will build specialized tools that address the peculiarities of each RNA type and accurately mine isomiRs, tRFs, and rRFs from human and mouse RNA-seq data. The tools will be robust, self-contained, and user-friendly. In Aim 2, we will build specialized databases to organize and provide easy access to information about isomiRs, tRFs, and rRFs that we have already compiled by mining 50,000 public datasets. In Aim 3, we will build a system that auto-identifies newly-added datasets to NIH’s SRA, profiles and annotates each dataset’s isomiRs, tRFs, and rRFs, and updates the databases with the new infor- mation each month. In Aim 4, we will create educational material describing best practices to help researchers benefit maximally from this framework, and build a system to allow them to interact with one another and submit their feedback. Lastly, we will validate experimentally select small RNAs implicated in breast cancer metastasis.

该项目侧重于三类小型RNA：已知的microRNA（miRNA）的同工型作为Isomirs；源自转移RNA（TRNA）的片段，称为TRF；而且，碎片 - 源自核糖体RNA（RRNA）的晶状体被称为RRF。 Isomir，TRF和RRF具有一些重要的特性，需要其详细的研究：（1）他们说明对于一个细胞中的所有小RNA的约80％。（2）它们调节Messenger RNA（mRNA）和Pro-的抽象 Teins。（3）它们的表达模式取决于细胞“上下文”（例如，组织类型，疾病类型）。（4）在hu-中男人，他们的表达模式还取决于“个人属性”（例如性，遗传血统，年龄）。要正确地挖掘RNA-seq数据中的Isomirs，TRF和RRF，理想工具必须解决几个符合条件交易因素。首先，可以由不同的父母RNA产生相同的短序列（例如TRF）。这些父母 RNA可以属于相同的子类型（例如，同一tRNA的不同tRNA iSodeCoder）或不同的子类型（例如，来自不同tRNA IsoAcceptor的Isodecoder）。其次，许多iso-的序列 MiR，TRF和RRF也可以在基因组的无关区域中找到。第三，副产品和/或不完整 miRNA，trNA和rRNA的副本，包括人类和包括人类在内的许多生物的核基因组老鼠。这些复杂因素的细节特定于RNA类型和基因组。最后，理想的工具必须特定于目标基因组。复杂因素和对基因组特异性的需求才在文献中才出现。作为结果，迄今为止，大多数可用的工具都是通用的，并且无法解释这些并发症。不是令人惊讶的是，大多数可用的数据库都是使用通用工具构建的。没有意识到基础缺点，许多研究人员了解了这些工具和数据库提供的信息的信息实验并分析其数据。反过来，这导致许多发表的文章无意间描述对分子的不明确价值的发现，并非总是Isomirs，trfs或rrfs。我们将解决这些差距如下。在AIM 1中，我们将建立专门的工具来解决特殊性每种RNA类型，并从人和小鼠RNA-seq数据中准确地挖掘Isomirs，TRF和RRF。这工具将是强大的，具有独立的和用户友好的。在AIM 2中，我们将构建专门的数据库来组织并轻松访问有关我们已经通过采矿进行编译的Isomirs，trfs和RRF的信息 50,000个公共数据集。在AIM 3中，我们将构建一个系统，该系统可以自动确定新添加的数据集，以达到NIH的SRA，配置和注释每个数据集的Isomirs，trfs和rrfs，并使用新的Infor-更新数据库每个月。在AIM 4中，我们将创建描述最佳实践的教育材料，以帮助研究人员从这个框架中获得最大的好处，并建立一个系统以允许他们相互互动并提交他们的反馈。最后，我们将验证实验选择在乳腺癌转移中实施的小型RNA。