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RNA Structure01:23

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Related Experiment Video

Updated: Feb 7, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.

Bernhard C Thiel1, Roman Ochsenreiter2, Veerendra P Gadekar3

  • 1Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria. thiel@tbi.univie.ac.at.

Genes
|August 4, 2018
PubMed
Summary
This summary is machine-generated.

This study computationally identified over 100,000 conserved RNA structures across vertebrates, revealing novel regulatory elements within transposable elements and noncoding RNAs. These findings enhance our understanding of RNA

Keywords:
RNA regulationRNA secondary structureRNAzconserved RNA structure elementsstructural alignment

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Area of Science:

  • Computational Biology
  • Genomics
  • RNA Biology

Background:

  • Functional RNA structures play critical roles in gene regulation.
  • Identifying conserved RNA structures across species is essential for understanding their biological significance.
  • Transposable elements and low-complexity regions are often overlooked for harboring regulatory RNA elements.

Purpose of the Study:

  • To computationally screen for conserved functional RNA structures in vertebrate genomes.
  • To investigate the potential of transposable elements and repeat regions in generating regulatory RNA elements.
  • To provide a comprehensive catalog of identified RNA structures accessible via a genome browser.

Main Methods:

  • Genome-wide screening of mouse (mm10) against 59 vertebrate alignments using RNAz-2.
  • Refinement of candidate loci using LocARNA-P.
  • Inclusion of masked repeat regions and a four-step analysis pipeline.

Main Results:

  • Over 100,000 conserved RNA structure elements were identified.
  • Enrichment of structures in 3'-untranslated regions (3'-UTRs) and small noncoding RNAs; depletion in coding sequences.
  • Approximately 95% of homologous loci are repeat-associated, primarily in intronic and intergenic regions.

Conclusions:

  • The study successfully identified a large number of conserved RNA structures, including novel elements in noncoding and repeat regions.
  • Findings highlight the regulatory potential of sequences within transposable elements and 3'-UTRs.
  • A custom UCSC genome browser trackhub provides open access to all identified RNA structures.