5LSN

SINEB2 element of the long non-coding RNA activator of translation AS Uchl1

  • Classification: RNA
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2016-09-05 Released: 2017-09-20 
  • Deposition Author(s): Podbevsek, P., Plavec, J.
  • Funding Organization(s): S.H.A.R.M.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1.

Podbevsek, P.Fasolo, F.Bon, C.Cimatti, L.Reisser, S.Carninci, P.Bussi, G.Zucchelli, S.Plavec, J.Gustincich, S.

(2018) Sci Rep 8: 3189-3189

  • DOI: 10.1038/s41598-017-14908-6
  • Primary Citation of Related Structures:  
    5LSN

  • PubMed Abstract: 
  • Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs ...

    Pervasive transcription of mammalian genomes leads to a previously underestimated level of complexity in gene regulatory networks. Recently, we have identified a new functional class of natural and synthetic antisense long non-coding RNAs (lncRNA) that increases translation of partially overlapping sense mRNAs. These molecules were named SINEUPs, as they require an embedded inverted SINE B2 element for their UP-regulation of translation. Mouse AS Uchl1 is the representative member of natural SINEUPs. It was originally discovered for its role in increasing translation of Uchl1 mRNA, a gene associated with neurodegenerative diseases. Here we present the secondary structure of the SINE B2 Transposable Element (TE) embedded in AS Uchl1. We find that specific structural regions, containing a short hairpin, are required for the ability of AS Uchl1 RNA to increase translation of its target mRNA. We also provide a high-resolution structure of the relevant hairpin, based on NMR observables. Our results highlight the importance of structural determinants in embedded TEs for their activity as functional domains in lncRNAs.


    Organizational Affiliation

    Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy. stefano.gustincich@iit.it.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (29-MER)A 29Mus musculus
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 5LSN Olderado

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
S.H.A.R.M.ItalyFP1123744003

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection