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. 2016 Jan 4;44(D1):D259-65.
doi: 10.1093/nar/gkv1036. Epub 2015 Oct 12.

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

Wen-Ju Sun  1 , Jun-Hao Li  1 , Shun Liu  1 , Jie Wu  1 , Hui Zhou  1 , Liang-Hu Qu  2 , Jian-Hua Yang  3
Affiliations

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

V体育官网 - Wen-Ju Sun et al. Nucleic Acids Res. .

V体育ios版 - Abstract

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 VSports手机版. 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. .

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Figures

Figure 1.
Figure 1.
System overview of RMBase core framework. We integrated a large set of RNA modification sites generated by 18 independent studies to profile the comprehensive genome-wide modification landscape of more than 100 types of RNA modifications. Integrative analysis of RNA modification sites has shown extensive post-transcriptional modification of RNA. Our combined analysis of RNA modification data with GWAS and miRNA target data identified thousands of miRNA targets and disease-related SNPs resided in the modification sites. High-throughput modification sequencing data were mapped to genomes and displayed in genome browser. All results generated by RBMBase are deposited in MySQL relational databases and displayed in the visual browser and web page.
Figure 2.
Figure 2.
Illustrative screen shots from the RMBase genome browser. RMBase genome browser provides an integrated view of modification sequencing data, aligned sequencing reads, RNA modification sites, protein-coding genes, ncRNA genes.
See this image and copyright information in PMC

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