Using RNA inverse folding to identify IRES-like structural subdomains

@article{Dot2013UsingRI,
  title={Using RNA inverse folding to identify IRES-like structural subdomains},
  author={Iv{\'a}n Dot{\'u} and Gloria Lozano and Peter Clote and Encarnaci{\'o}n Mart{\'i}nez-Salas},
  journal={RNA Biology},
  year={2013},
  volume={10},
  pages={1842 - 1852}
}
Internal ribosome entry site (IRES) elements govern protein synthesis of mRNAs that bypass cap-dependent translation inhibition under stress conditions. Picornavirus IRES are cis-acting elements, organized in modular domains that recruit the ribosome to internal mRNA sites. The aim of this study was to retrieve short RNA sequences with the capacity to adopt RNA folding patterns conserved with IRES structural subdomains, likely corresponding to RNA modules. We have applied a new program… 
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20 Citations
Background Citations
4
Methods Citations
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20 Citations

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Citation Type

Structural insights into viral IRES-dependent translation mechanisms.
IRES Elements: Issues, Controversies and Evolutionary Perspectives
TLDR
Understanding of the structural motifs important for IRES function could greatly improve the accuracy to predict IRES-like motifs hidden in genome sequences and to decipher the evolutionary history of these regulatory elements.
Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements
TLDR
The feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function is shown.
Insights into Structural and Mechanistic Features of Viral IRES Elements
TLDR
This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements and could improve the accuracy to predict IRES-like motifs hidden in genome sequences.
Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences
TLDR
Evidence is reviewed suggesting that model IRES elements consist of the combination of short modules, providing sites of interaction for ribosome subunits, eIFs and RBPs, with implications for definition of criteria to identify novel IRES-like elements genome wide.
Modeling Three-Dimensional Structural Motifs of Viral IRES.
Picornavirus IRES elements: RNA structure and host protein interactions.
Magnesium‐dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction
TLDR
It is shown that the IRES element adopts a near‐native structure in the absence of proteins, shedding light on the influence of Mg2+ ions on the local flexibility and binding of eIF4G in a model IRES elements.
A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites
TLDR
The crystal structure of domain V from the IRES of hepatitis A virus (HAV) ssRNA genome is reported, suggesting that the functional homology among different types of picornaviral IRESs is structure-based.
RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures
TLDR
This review aims to summarize the processes in which viral RNA structures have been found to play an active role in translational regulation, their global conformational features and the bioinformatics/computational tools available for the identification and prediction of these structures.
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TLDR
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