RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data.
RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data.
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RBase：从高通量测序数据中解码 RNA 修饰景观的资源
DOI：
10.1093/nar/gkv1036
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Yang JH
中科院分区：
文献类型：
--
作者：
Sun WJ;Li JH;Liu S;Wu J;Zhou H;Qu LH;Yang JH
尽管所有生物体中已有超过 100 种不同类型的 RNA 修饰特征，但令人惊讶的是，人们对修饰位置及其功能知之甚少。最近，已经开发了各种高通量修饰测序方法来识别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 RBase（RNA 修饰库，http://mirlab.sysu.edu.cn/rmbase/），用于解码从 18 项独立研究生成的高通量修饰数据中识别出的 RNA 修饰的全基因组景观。当前版本的 RBase 包括从 Pseudo-seq 和 CeU-seq 测序数据生成的~9500 个伪尿苷 (Ψ) 修饰、从 Aza-IP 数据预测的~1000 个 5-甲基胞嘧啶 (m5C)、从 m6A-seq 发现的~124 200 个 N6-甲基腺苷 (m6A) 修饰和~1210 个 2'-O-甲基化从 RiboMeth-seq 数据和公共资源中鉴定出 (2′-O-Me)。此外，RBase 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。它提供网络界面来显示 RNA 修饰位点和 microRNA 靶位点之间的数千种关系。它还可用于说明修饰位点/区域中与疾病相关的 SNP。 RBase 提供基因组浏览器和基于 Web 的 modTool 来查询、注释和可视化各种 RNA 修饰。该数据库将有助于扩大我们对 RNA 修饰潜在功能的理解。
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 (m5C) predicted from Aza-IP data, ∼124 200 N6-Methyladenosine (m6A) modifications discovered from m6A-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.