Nucleic acids research, 2018-01, Vol.46 (D1), p.D327-D334
2018
Volltextzugriff (PDF)
Details
- Autor(en) / Beteiligte
- Titel
- RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data
- Ist Teil von
- Nucleic acids research, 2018-01, Vol.46 (D1), p.D327-D334
- Ort / Verlag
- England
- Erscheinungsjahr
- 2018
- Quelle
- MEDLINE
- Beschreibungen/Notizen
- 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.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 0305-1048eISSN: 1362-4962DOI: 10.1093/nar/gkx934Titel-ID: cdi_pubmed_primary_29040692
- Format
- –
- Schlagworte
- 5-Methylcytosine - metabolism, Adenosine - analogs & derivatives, Adenosine - metabolism, Animals, Binding Sites, Databases, Genetic, Disease - genetics, Gene Expression Profiling, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Mice, MicroRNAs - metabolism, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Pseudouridine - metabolism, Rats, RNA Processing, Post-Transcriptional, RNA, Long Noncoding - chemistry, RNA, Long Noncoding - metabolism, RNA-Binding Proteins - metabolism, Sequence Analysis, RNA, User-Computer Interface