RNAcentral, the RNA sequence database

RNAcentral，RNA 序列数据库

• 批准号: BB/N019199/1
• 负责人: Alex Bateman
• 金额: $ 87.33万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN019199%2F1
• 关键词: RNAcentral; RNA; sequence; database

In molecular biology, the central dogma explains that the genes in DNA code for RNA. RNA molecules are then translated into proteins that are the mini-machines that carry out the main processes in the cell. Recently it has become apparent that potentially many thousands of human genes code for RNAs that are not translated into proteins, but rather carry out important functions in the cell as RNA. These molecules are often known as non-coding RNAs. Much of the focus in biology over the past thirty years of research has been on DNA and proteins, but recently there has been a surge of interest in non-coding RNAs. In fact, the core of the machine that makes proteins from RNA, called the ribosome, has itself been shown to be made of RNA. Non-coding RNAs have also been shown to be widely involved in regulating the levels of other genes and may be useful in making treatments for patients with a variety of diseases. The role of non-coding RNAs in plant and animal development is evident, but a deeper understanding of the biology is essential, thereby allowing their modulation to enhance features such as yield or resistance to diseases. Unsurprisingly, aberrant expression of non-coding RNAs has also been implicated in numerous disease states.Research and innovation in the area of non-coding RNAs, and in molecular biology more generally, is hampered by the lack of an authoritative and complete resource collecting together all known non-coding RNAs. There are over 30 different online databases that contain information about different types of RNA molecules. Each of these resources makes their information available in different ways. The scattered nature of these resources has made it nearly impossible for biologists to discover what is known about non-coding RNAs related to their research area. To address this problem we created a resource called RNAcentral that brings together information from all the different RNA databases in one place. The most important information stored in RNAcentral is called the sequence of the RNA. Many existing RNA resources (called RNAcentral Expert Databases) have provided their data to RNAcentral. In this proposal we will add further more detailed information about the structure and function of RNAs into RNAcentral. We will work closely with one specific expert database, called miRBase, based at the University of Manchester, who will test out the system for searching the RNAcentral sequence database on specific subsets of RNAs. By the end of this project, researchers from around the UK and the rest of the world will have access to an increased set of information about RNAs. This information will be freely available in a variety of ways including via a website and as a downloadable database. Having access to this information will help researchers connect RNAs into their work better to help them make new discoveries sooner.

在分子生物学中，中央教条解释了RNA的DNA代码中的基因。然后将RNA分子转换为蛋白质，这些蛋白是在细胞中进行主要过程的迷你机器。最近，很明显，可能成千上万的人类基因代码的RNA代码未转化为蛋白质，而是在细胞中以RNA的形式执行重要功能。这些分子通常被称为非编码RNA。在过去的三十年中，生物学的重点是DNA和蛋白质的重点，但最近对非编码RNA引起了人们的兴趣。实际上，从RNA（称为核糖体）生产蛋白质的机器的核心本身已被证明是由RNA制成的。非编码RNA也已被证明广泛参与调节其他基因水平，并且可能有助于为各种疾病的患者进行治疗。非编码RNA在动植物发育中的作用是显而易见的，但是对生物学的更深入了解是必不可少的，从而使它们的调节能够增强诸如产量或对疾病的抗性之类的特征。毫不奇怪的是，非编码RNA的异常表达也与许多疾病状态有关。研究和创新非编码RNA领域，并且在更普遍的分子生物学领域中，由于缺乏权威和完整的资源收集而受到阻碍。所有已知的非编码RNA。有30多个不同的在线数据库包含有关不同类型的RNA分子的信息。这些资源中的每一个都以不同的方式提供其信息。这些资源的分散性质使生物学家几乎不可能发现与其研究领域相关的非编码RNA的了解。为了解决这个问题，我们创建了一个称为rnacentral的资源，该资源将来自一个地方的所有不同RNA数据库的信息汇总在一起。存储在rnacentral中的最重要信息称为RNA的序列。许多现有的RNA资源（称为rnacentral专家数据库）已将其数据提供给rnacentral。在此提案中，我们将在rnacentral中添加有关RNA的结构和功能的更多详细信息。我们将与位于曼彻斯特大学的一个特定专家数据库密切合作，该数据库称为Mirbase，该数据库将测试该系统，以搜索RNAS特定子集的rnacentral序列数据库。到该项目结束时，来自英国和世界其他地区的研究人员将获得有关RNA的越来越多的信息。此信息将以多种方式免费提供，包括通过网站和可下载的数据库。访问此信息将帮助研究人员更好地将RNA连接到他们的工作中，以帮助他们更快地进行新发现。

项目成果

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.

• DOI: 10.1093/nar/gkaa921
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: RNAcentral Consortium

The European Nucleotide Archive in 2020.

• DOI: 10.1093/nar/gkaa1028
• 发表时间: 2021-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Harrison PW;Ahamed A;Aslam R;Alako BTF;Burgin J;Buso N;Courtot M;Fan J;Gupta D;Haseeb M;Holt S;Ibrahim T;Ivanov E;Jayathilaka S;Balavenkataraman Kadhirvelu V;Kumar M;Lopez R;Kay S;Leinonen R;Liu X;O'Cathail C;Pakseresht A;Park Y;Pesant S;Rahman N;Rajan J;Sokolov A;Vijayaraja S;Waheed Z;Zyoud A;Burdett T;Cochrane G
• 通讯作者: Cochrane G

RNAcentral: a hub of information for non-coding RNA sequences.

• DOI: 10.1093/nar/gky1034
• 发表时间: 2019-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: The RNAcentral Consortium

R2DT is a framework for predicting and visualising RNA secondary structure using templates.

• DOI: 10.1038/s41467-021-23555-5
• 发表时间: 2021-06-09
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Sweeney BA;Hoksza D;Nawrocki EP;Ribas CE;Madeira F;Cannone JJ;Gutell R;Maddala A;Meade CD;Williams LD;Petrov AS;Chan PP;Lowe TM;Finn RD;Petrov AI
• 通讯作者: Petrov AI

The European Nucleotide Archive in 2018.

• DOI: 10.1093/nar/gky1078
• 发表时间: 2019-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Harrison PW;Alako B;Amid C;Cerdeño-Tárraga A;Cleland I;Holt S;Hussein A;Jayathilaka S;Kay S;Keane T;Leinonen R;Liu X;Martínez-Villacorta J;Milano A;Pakseresht N;Rajan J;Reddy K;Richards E;Rosello M;Silvester N;Smirnov D;Toribio AL;Vijayaraja S;Cochrane G
• 通讯作者: Cochrane G