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 (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.
Highlights
Post-transcriptional modification of RNA molecules occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs [1,2,3,4,5]
More than 100 types of RNA modifications have been described so far, most of them were thought to be abundant in tRNAs, rRNAs and snRNAs, but rare in mRNAs and in regulatory non-coding RNAs
Known modifications for rRNAs, snRNAs and tRNAs were extracted from snoRNABase [25], MODOMICS [26], Yeast snoRNA Database [27] as well as other literature sources [28,29,30], and were mapped to genome using Bowtie program [24] to determine the genomic coordinates and construct the genome-wide landscape of RNA modifications
Summary
Post-transcriptional modification of RNA molecules occurs in all living organisms, and is one of the most evolutionarily conserved properties of RNAs [1,2,3,4,5]. To determine the transcriptome-wide landscape of RNA modifications, recently many studies have developed highthroughput modification sequencing methods to identify diverse post-transcriptional modifications of RNA molecules [1,2,3,4,5]. Application of these methods has identified various modifications (e.g. pseudouridine, m6A, m5C, 2 -OMe) within coding and non-coding sequences at single nucleotide or very high resolution [6,7,8,9,10,11,12,13,14,15,16,17]. As the integration of more than 100 types of RNA modifications, it is expected to help the researchers to investigate the potential functions and mechanisms of RNA modifications
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
