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Related Concept Videos

Bacterial RNA Polymerase00:43

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Updated: Mar 10, 2026

Identification of Circular RNAs using RNA Sequencing
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Increased complexity of circRNA expression during species evolution.

Rui Dong1,2, Xu-Kai Ma1,2, Ling-Ling Chen3,2,4

  • 1a Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai , China.

RNA Biology
|December 17, 2016
PubMed
Summary

Species-specific circular RNA (circRNA) expression patterns arise from complementary sequences in flanking introns, not the circRNAs themselves. Short interspersed nuclear elements (SINEs), particularly Alu elements, significantly influence circRNA formation and evolution.

Keywords:
AluSINEback-splicingcircRNAcomplementary sequenceevolutionspecies-specific

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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
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In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Circular RNAs (circRNAs) are generated from precursor mRNA (pre-mRNA) via back-splicing.
  • circRNA expression exhibits cell- and tissue-specific patterns.
  • The mechanisms driving distinct circRNA expression across species are not fully understood.

Purpose of the Study:

  • To systematically compare circRNA expression between human and mouse.
  • To investigate the molecular basis for conserved and divergent circRNA expression.
  • To elucidate the role of intronic sequences in regulating circRNA formation.

Main Methods:

  • Comparative analysis of circRNA expression profiles in human and mouse.
  • Identification and characterization of complementary sequences in flanking introns.
  • Development and application of the Complementary Sequence Index (CSI) to quantify RNA pairing capacity.

Main Results:

  • Only a small subset of human circRNAs are conserved in mouse.
  • Conserved circRNA expression correlates with orientation-opposite complementary sequences in flanking introns.
  • Short interspersed nuclear elements (SINEs), especially human Alu elements, are major contributors to circRNA formation.
  • Diverse distribution of SINEs across species contributes to complex circRNA expression evolution.

Conclusions:

  • circRNA expression is species-specific, influenced by intronic sequence features.
  • Complementary sequences in introns, particularly SINEs, play a crucial role in regulating circRNA biogenesis.
  • This study provides a reference catalog of circRNAs and highlights the impact of SINEs on gene expression regulation.