A Reference Transcript Database for improved analysis of RNA-seq data from barley

用于改进大麦 RNA-seq 数据分析的参考转录本数据库

• 批准号: BB/R014582/1
• 负责人: Robbie Waugh
• 金额: $ 40.53万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR014582%2F1
• 关键词: Reference; Transcript; Database; improved; analysis

The term 'gene expression' refers to the biological process by which a gene gives rise to a protein. In eukaryotes, gene expression is complex. The DNA sequence of the gene is first copied into a precursor messenger RNA (pre-mRNA) by the process of transcription and the pre-mRNA subjected to several processing steps to form a mature messenger RNA (mRNAs) that is the template for synthesis of the corresponding protein. The post-transcriptional processing steps can generate different mRNA transcripts from the same gene (i.e. transcript isoforms), effectively modulating individual transcript abundance and potentially protein function. Having multiple transcript isoforms from a single gene is problematic in terms of 1) defining the expression levels of individual transcript isoforms and how they change under different conditions, and 2) determining their characteristics - such as whether they encode protein isoforms or not. As gene expression data is widely used to derive biological inference, for example, by grouping genes according to common patterns of expression, failure to take account of the relative abundance of alternative transcripts will unavoidably generate false conclusions. In this project, we focus on the development of a resource/tool that will allow the accurate detection and quantification of mRNA transcript isoforms in barley. The tool will enable high resolution analysis of dynamic changes in gene expression at the individual transcript level and as a recognised and accessible reference will help unify and structure such analyses across a research community. One of the main approaches scientists use to associate genes with functions is to monitor patterns of gene expression: i.e. where and when genes are switched on or off, and at what level. Current approaches provide an overall measure of gene expression by counting the frequency of occurrence of very specific sequences that correspond to a given mRNA relative to the whole population of mRNAs in a particular sample and transforming these counts into relative abundance levels. However these methods are unable to distinguish the abundance of individual isoform variants, in particular those that determine protein levels, structures and activities. We call the tool a 'Reference Transcript Database' or RTD. The RTD is effectively a library of all of the transcript isoforms that exist in a diverse range of tissues from a single organism. By using the RTD in gene expression studies we can identify and determine the abundance of different transcript isoforms easily and quickly, and these can be used in subsequent functional analyses.We focus this project on the crop plant, barley, a model for the small grain Triticeae cereals that include wheat and rye. The RTD will allow effects on global and specific gene expression to be easily analysed at the transcript level in plants subjected to a range of conditions or treatments, improving our community's ability to explore and understand a wide range of biological processes. The RTD will be refreshed and maintained longer term by the barley and computational sciences groups at the James Hutton Institute.

“基因表达”一词指的是基因产生蛋白质的生物学过程。在真核生物中，基因表达是复杂的。基因的DNA序列首先通过转录过程被复制成前体信使RNA (pre-mRNA)，前体信使RNA经过几个加工步骤形成成熟的信使RNA (mrna)，这是合成相应蛋白质的模板。转录后处理步骤可以从同一基因产生不同的mRNA转录物（即转录异构体），有效地调节个体转录物丰度和潜在的蛋白质功能。拥有来自单个基因的多个转录异构体在以下方面存在问题：1)定义单个转录异构体的表达水平以及它们在不同条件下如何变化；2)确定它们的特征——例如它们是否编码蛋白质异构体。由于基因表达数据被广泛用于推导生物学推断，例如，通过根据共同的表达模式对基因进行分组，如果不考虑替代转录本的相对丰度，将不可避免地产生错误的结论。在这个项目中，我们的重点是开发一个资源/工具，将允许准确检测和定量的mRNA转录异构体在大麦。该工具将能够在个体转录水平上对基因表达的动态变化进行高分辨率分析，并且作为一个公认的和可访问的参考，将有助于统一和构建整个研究社区的此类分析。科学家们用来将基因与功能联系起来的主要方法之一是监测基因表达的模式：即基因在何时何地开启或关闭，以及在什么水平上。目前的方法是通过计算特定样本中相对于整个mRNA群体的特定序列的出现频率，并将这些计数转换为相对丰度水平，从而提供基因表达的总体测量。然而，这些方法无法区分个体异构体变异的丰度，特别是那些决定蛋白质水平、结构和活性的异构体。我们称这个工具为“参考成绩单数据库”或RTD。RTD是一个有效的文库，包含了来自单一生物体的多种组织中存在的所有转录本同种异构体。通过在基因表达研究中使用RTD，我们可以方便、快速地识别和确定不同转录物异构体的丰度，并为后续的功能分析提供依据。我们把这个项目的重点放在农作物大麦上，大麦是小麦和黑麦等小粒小麦的典范。RTD将允许在转录水平上容易地分析受一系列条件或处理的植物中对全局和特定基因表达的影响，从而提高我们社区探索和理解广泛生物过程的能力。RTD将由詹姆斯·赫顿研究所（James Hutton Institute）的大麦和计算科学小组更新和长期维护。

项目成果

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.

• DOI: 10.1080/15476286.2020.1858253
• 发表时间: 2021-11
• 期刊: RNA biology
• 影响因子: 4.1
• 作者: Guo W;Tzioutziou NA;Stephen G;Milne I;Calixto CP;Waugh R;Brown JWS;Zhang R
• 通讯作者: Zhang R

The value of genotype-specific reference for transcriptome analyses in barley.

• DOI: 10.26508/lsa.202101255
• 发表时间: 2022-08
• 期刊: LIFE SCIENCE ALLIANCE
• 影响因子: 4.4
• 作者: Guo, Wenbin;Coulter, Max;Waugh, Robbie;Zhang, Runxuan
• 通讯作者: Zhang, Runxuan

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

3D RNA-seq：强大而灵活的工具，可为生物学家快速准确地进行 RNA-seq 数据的差异表达和选择性剪接分析

• DOI: 10.6084/m9.figshare.13450554
• 发表时间: 2020
• 作者: Guo W

EoRNA, a barley gene and transcript abundance database

EoRNA，大麦基因和转录本丰度数据库

• DOI: 10.1101/2020.11.24.395749
• 发表时间: 2020
• 作者: Milne L

A powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

• DOI: 10.1101/656686
• 发表时间: 2019-05
• 期刊: bioRxiv
• 作者: Wenbin Guo;Nikoleta A Tzioutziou;Gordon Stephen;Iain Milne;C. Calixto;R. Waugh;John W. S. Brown