Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • The landscape of RNA modifications from high-throughput sequencing data

    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

    Last edited by rnaNGS; 09-01-2017, 02:15 AM. Reason: update datasets

  • #2
    about 101,780 novel m6A modification sites from 4 studies (m6A-CLIP, m6A-Seq technologies) have been added into RMBase.
    Last edited by rnaNGS; 09-01-2017, 02:15 AM.

    Comment


    • #3
      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.

      Comment


      • #4
        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
        Last edited by rnaNGS; 09-01-2017, 02:16 AM.

        Comment


        • #5
          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.

          Comment


          • #6
            RMBase v2.0 has been developed, RMBase v2.0 is freely available at http://rna.sysu.edu.cn/rmbase/

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            8 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            8 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            49 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X