Sun Wen-Ju, Li Jun-Hao, Liu Shun, Wu Jie, Zhou Hui, Qu Liang-Hu, Yang Jian-Hua
Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P. R. China.
Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, P. R. China State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P. R. China
Nucleic Acids Res. 2016 Jan 4;44(D1):D259-65. doi: 10.1093/nar/gkv1036. Epub 2015 Oct 12.
Although more than 100 different types of RNA modifications have been characterized across all living organisms, surprisingly little is known about the modified positions and their functions. Recently, various high-throughput modification sequencing methods have been developed to identify diverse post-transcriptional modifications of RNA molecules. In this study, we developed a novel resource, RMBase (RNA Modification Base, http://mirlab.sysu.edu.cn/rmbase/), to decode the genome-wide landscape of RNA modifications identified from high-throughput modification data generated by 18 independent studies. The current release of RMBase includes ∼ 9500 pseudouridine (Ψ) modifications generated from Pseudo-seq and CeU-seq sequencing data, ∼ 1000 5-methylcytosines (m(5)C) predicted from Aza-IP data, ∼ 124 200 N6-Methyladenosine (m(6)A) modifications discovered from m(6)A-seq and ∼ 1210 2'-O-methylations (2'-O-Me) identified from RiboMeth-seq data and public resources. Moreover, RMBase provides a comprehensive listing of other experimentally supported types of RNA modifications by integrating various resources. It provides web interfaces to show thousands of relationships between RNA modification sites and microRNA target sites. It can also be used to illustrate the disease-related SNPs residing in the modification sites/regions. RMBase provides a genome browser and a web-based modTool to query, annotate and visualize various RNA modifications. This database will help expand our understanding of potential functions of RNA modifications.
尽管在所有生物中已鉴定出100多种不同类型的RNA修饰，但令人惊讶的是，对于修饰位点及其功能却知之甚少。最近，已开发出各种高通量修饰测序方法来鉴定RNA分子的多种转录后修饰。在本研究中，我们开发了一种新资源RMBase（RNA修饰数据库，http://mirlab.sysu.edu.cn/rmbase/），以解读从18项独立研究产生的高通量修饰数据中鉴定出的全基因组RNA修饰图谱。RMBase的当前版本包括从假尿嘧啶测序（Pseudo-seq）和CeU测序数据产生的约9500个假尿嘧啶（Ψ）修饰、从氮杂环丙烷-IP（Aza-IP）数据预测的约1000个5-甲基胞嘧啶（m(5)C）、从m(6)A测序发现的约124200个N6-甲基腺苷（m(6)A）修饰以及从核糖甲基化测序（RiboMeth-seq）数据和公共资源鉴定出的约1210个2'-O-甲基化（2'-O-Me）。此外，RMBase通过整合各种资源提供了其他实验支持的RNA修饰类型的全面列表。它提供了网络界面来展示RNA修饰位点与微小RNA靶位点之间的数千种关系。它还可用于阐明位于修饰位点/区域的疾病相关单核苷酸多态性。RMBase提供了一个基因组浏览器和一个基于网络的modTool，用于查询、注释和可视化各种RNA修饰。该数据库将有助于扩展我们对RNA修饰潜在功能的理解。
