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

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, researchers at Sun Yat-sen University have developed a novel resource, RMBase (RNA Modification Base), 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.

System overview of RMBase core framework. The devlopers 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. Their 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.

Availability – RMBase is accessible at: http://mirlab.sysu.edu.cn/rmbase/