SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
The landscape of RNA modifications from high-throughput sequencing data rnaNGS Bioinformatics 5 09-01-2017 02:17 AM
PubMed: Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Co Newsbot! Literature Watch 0 03-22-2013 02:00 AM

Reply
 
Thread Tools
Old 10-16-2015, 07:43 PM   #1
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 64
Default Decoding the landscape of RNA modifications from transcriptome sequencing data

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


Last edited by yjhua2110; 09-05-2017 at 04:16 PM.
yjhua2110 is offline   Reply With Quote
Old 10-28-2015, 03:45 AM   #2
rnaNGS
Member
 
Location: China

Join Date: Dec 2009
Posts: 41
Default

101,780 novel m6A sites from 4 studies (m6A-CLIP, m6A-Seq technologies) have been added into RMBase.
rnaNGS is offline   Reply With Quote
Old 02-29-2016, 04:18 PM   #3
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 64
Default

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 is offline   Reply With Quote
Old 07-14-2016, 01:34 AM   #4
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 64
Default 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.

Last edited by yjhua2110; 09-05-2017 at 04:16 PM.
yjhua2110 is offline   Reply With Quote
Old 12-17-2016, 09:00 PM   #5
rnaNGS
Member
 
Location: China

Join Date: Dec 2009
Posts: 41
Default 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 is offline   Reply With Quote
Old 02-25-2017, 01:30 AM   #6
rnaNGS
Member
 
Location: China

Join Date: Dec 2009
Posts: 41
Default 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
rnaNGS is offline   Reply With Quote
Old 09-05-2017, 04:17 PM   #7
yjhua2110
Member
 
Location: china

Join Date: Nov 2009
Posts: 64
Default

RMBase v2.0 has been developed, RMBase v2.0 is freely available at http://rna.sysu.edu.cn/rmbase/
yjhua2110 is offline   Reply With Quote
Reply

Tags
m6a, mirna, rna modification, rna-seq, snp

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO