The landscape of RNA modifications from high-throughput sequencing data

[rnaNGS]

We're pleased to announce the release of the RMBase (RNA Modification Base) for decoding the landscape of RNA modifications identified from 404 high-throughput 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.

We hope 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/. We are looking forward to hearing your feedback!

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

[rnaNGS]

about 101,780 novel m6A modification 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.

This datasets will be added into RMBase.

[rnaNGS]

RNA modification Database and RNA-Binding Protein Binding Sites

Recently, we integrated thousands of RNA-Binding Proteins (RBP) binding sites identified from CLIP-Seq experiments and performed relationship analysis of RBP binding regions and RNA modifications. RMBase demonstrated thousands of RNA modifications located within RNA-Binding Proteins (RBPs) regions and revealed that RNA modifications may influence the function of RBP or the RBP may catalyse the RNA modification.

You can browse various RNA modifications within the RNA-Binding Proteins (RBPs) Binding sites with follow website: http://rna.sysu.edu.cn/rmbase/modRBP.php

[yjhua2110]

RNA modifications in sex determination and nervous system

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]

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