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Identification of Circular RNAs using RNA Sequencing
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Short intronic repeat sequences facilitate circular RNA production.

Dongming Liang1, Jeremy E Wilusz2

  • 1Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA.

Genes & Development
|October 5, 2014
PubMed
Summary

Circular RNAs form from messenger RNA (mRNA) via a process called back-splicing. Specific intronic repeats and sequences guide the spliceosome to create these circular noncoding RNAs.

Keywords:
AluEPHB4HIPK3ZKSCAN1circRNAnoncoding RNAsplicing

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Genetics

Background:

  • Deep sequencing reveals thousands of circular noncoding RNAs (circRNAs) originating from protein-coding genes.
  • circRNAs are formed by a process called back-splicing, where the spliceosome joins the ends of an exon.
  • The precise mechanisms governing exon selection for circRNA formation remain largely unknown.

Purpose of the Study:

  • To elucidate the molecular mechanisms controlling exon selection during circRNA biogenesis.
  • To identify sequence and structural elements required for the formation of circular noncoding RNAs.

Main Methods:

  • Extensive mutagenesis of expression plasmids.
  • In vivo cellular assays to assess RNA circularization.
  • Analysis of intronic and exonic sequence requirements.

Main Results:

  • Short intronic inverted repeats (e.g., Alu elements) and splice sites are sufficient to promote exon circularization.
  • Intronic repeats must base-pair to juxtapose splice sites for circularization.
  • Exonic sequences, intronic repeats, and 3' end processing signals collaborate to regulate circRNA formation, indicating potential post-transcriptional events.

Conclusions:

  • Identified key sequence and structural motifs that drive circRNA biogenesis.
  • Proposed models for spliceosome-mediated exon selection in circRNA formation.
  • Highlighted the interplay between intronic repeats, exonic sequences, and processing signals in determining linear mRNA versus circRNA fate.