Decoding the landscape of RNA modifications from transcriptome sequencing data

[yjhua2110]

RMBase (RNA Modification Base) is a RNA modification database and designed for decoding the landscape of RNA modifications (>100 different RNA modification types) identified from 404 high-throughput RNA sequencing data (Pseudo-seq, Ψ-seq, CeU-seq, Aza-IP, MeRIP-seq, m6A-seq, miCLIP, m6A-CLIP, RiboMeth-seq).

It contains ~124200 N6-Methyladenosines (m6A), ~9500 pseudouridine (Ψ) modifications, ~1000 5-methylcytosine (m5C) modifications, ~1210 2′-O-methylations (2′-O-Me) and ~3130 other types of RNA modifications.

RMBase demonstrated thousands of RNA modifications located within regulatory RNAs (e.g. mRNAs, lncRNAs, miRNAs, pseudogenes, circRNAs, snoRNAs etc.), miRNA target sites and disease-related SNPs.

This platform will greatly help biologists to explore the prevalence, mechanism and function of various RNA modifications and link them with human cancers and other diseases.

RMBase is freely available at http://rna.sysu.edu.cn/rmbase/.

RMBase paper is available at http://nar.oxfordjournals.org/content/44/D1/D259

[rnaNGS]

101,780 novel m6A sites from 4 studies (m6A-CLIP, m6A-Seq technologies) have been added into RMBase.

[yjhua2110]

recently, one Nature paper and one Nature Chemical biology paper have identified dynamic N1-methyladenosine (m1A) methylome in the message RNAs (mRNAs) using newly developed sequencing approaches. these modifications indicate a functional role for m1A in promoting translation of methylated mRNA.
(1) The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016 Feb 25;530(7591):441-6.
(2) Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome.Nat Chem Biol. 2016 Feb 10.

[yjhua2110]

relationships between RNA-Binding Proteins and RNA modificaitons

millions of relationships between RNA-Binding Protein (RBP) binding regions and RNA modifications have been added into RMBase. We revealed that RNA modifications may influence the function of RBPs or the RBPs may catalyze the RNA modification.

A novel web-page modRBP has been added.

[rnaNGS]

RNA modifications and neuronal functions, sex determination

two papers published in nature journal discovered RNA modifications modulate neuronal functions and sex determination in Drosophila.
(1) Lence T et al. m(6)A modulates neuronal functions and sex determination in Drosophila. Nature. 2016 Dec 8;540(7632):242-247.
(2) Haussmann et al. m(6)A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature. 2016 Dec 8;540(7632):301-304.

[rnaNGS]

The RNA code comes into focus

two feature papers published in nature journal about RNA modifications.
(1) An epigenetics gold rush: new controls for gene expression
(2) The RNA code comes into focus

[yjhua2110]

RMBase v2.0 has been developed, RMBase v2.0 is freely available at http://rna.sysu.edu.cn/rmbase/