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Nucleic Acids Res. 2018 Jan 4;46(D1):D327-D334. doi: 10.1093/nar/gkx934.

RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.

Xuan JJ1,2, Sun WJ1,2, Lin PH1,2, Zhou KR1,2, Liu S1,2, Zheng LL1,2, Qu LH1,2, Yang JH1,2.

Author information

1
Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou 510275, PR China.
2
State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China.

Abstract

More than 100 distinct chemical modifications to RNA have been characterized so far. However, the prevalence, mechanisms and functions of various RNA modifications remain largely unknown. To provide transcriptome-wide landscapes of RNA modifications, we developed the RMBase v2.0 (http://rna.sysu.edu.cn/rmbase/), which is a comprehensive database that integrates epitranscriptome sequencing data for the exploration of post-transcriptional modifications of RNAs and their relationships with miRNA binding events, disease-related single-nucleotide polymorphisms (SNPs) and RNA-binding proteins (RBPs). RMBase v2.0 was expanded with ∼600 datasets and ∼1 397 000 modification sites from 47 studies among 13 species, which represents an approximately 10-fold expansion when compared with the previous release. It contains ∼1 373 000 N6-methyladenosines (m6A), ∼5400 N1-methyladenosines (m1A), ∼9600 pseudouridine (Ψ) modifications, ∼1000 5-methylcytosine (m5C) modifications, ∼5100 2'-O-methylations (2'-O-Me), and ∼2800 modifications of other modification types. Moreover, we built a new module called 'Motif' that provides the visualized logos and position weight matrices (PWMs) of the modification motifs. We also constructed a novel module termed 'modRBP' to study the relationships between RNA modifications and RBPs. Additionally, we developed a novel web-based tool named 'modMetagene' to plot the metagenes of RNA modification along a transcript model. This database will help researchers investigate the potential functions and mechanisms of RNA modifications.

PMID:
29040692
PMCID:
PMC5753293
DOI:
10.1093/nar/gkx934
[Indexed for MEDLINE]
Free PMC Article

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