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Identification of Circular RNAs using RNA Sequencing
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Circular code motifs near the ribosome decoding center.

Karim El Soufi1, Christian J Michel1

  • 1Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France.

Computational Biology and Chemistry
|November 8, 2015
PubMed
Summary

This study identifies novel circular code X motifs in ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) of prokaryotes and eukaryotes. These findings support a proposed translation code based on circular codes, enhancing our understanding of gene expression.

Keywords:
Circular code motifRibosomal RNATransfer RNATranslation code

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • A maximal C(3) self-complementary trinucleotide circular code X is found in genes across various organisms.
  • Previous work identified X circular code motifs (X motifs) in ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), including specific motifs in the ribosome decoding center.
  • Three universal X motifs (mAA, mG, m) were previously identified in the ribosome decoding center.

Purpose of the Study:

  • To extend the identification of X motifs in rRNAs of prokaryotes and eukaryotes near the ribosome decoding center.
  • To further analyze the occurrence and properties of X motifs in prokaryotic and eukaryotic tRNAs.
  • To strengthen the concept of a translation code based on the circular code.

Main Methods:

  • Identification of X motifs in prokaryotic 16S rRNAs and eukaryotic 18S rRNAs near the ribosome decoding center.
  • Statistical analysis of X motifs in large tRNA populations from prokaryotes and eukaryotes, considering taxonomy, length, and score.
  • Characterization of the occurrence probabilities and properties of identified X motifs in tRNAs.

Main Results:

  • Seven X motifs (PrRNAXm) conserved in prokaryotic 16S rRNAs and four X motifs (ErRNAXm) conserved in eukaryotic 18S rRNAs were identified near the ribosome decoding center.
  • Statistical analysis revealed that X motifs have higher occurrence probabilities in the 5' and/or 3' regions of prokaryotic and eukaryotic tRNAs than expected by chance.
  • Numerous large X motifs (≥ 9 nucleotides), including very large ones (≥ 20 nucleotides), were found in prokaryotic tRNAs, with some properties described.

Conclusions:

  • The identification of conserved X motifs in rRNAs near the decoding center and the prevalence of large X motifs in tRNAs provide further evidence for the proposed translation code.
  • These findings reinforce the significance of circular codes in fundamental biological processes like translation.
  • The study strengthens the concept of a translation code based on circular codes, as proposed by Michel (2012).