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Identification of Circular RNAs using RNA Sequencing
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Quantifying full-length circular RNAs in cancer.

Ken Hung-On Yu1,2, Christina Huan Shi2, Bo Wang1

  • 1Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.

Genome Research
|October 19, 2021
PubMed
Summary

This study introduces psirc, a novel method for identifying full-length circular RNA (circRNA) isoforms and their expression levels. psirc reveals alternatively spliced circRNAs with significantly higher expression and altered miRNA binding potential in nasopharyngeal carcinoma.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Circular RNAs (circRNAs) are prevalent in cancers and exhibit stability due to exonuclease resistance.
  • Alternative splicing generates diverse circRNA isoforms with varying sequences and interaction capabilities.
  • Accurate circRNA functional studies necessitate the identification of complete circRNA sequences.

Purpose of the Study:

  • To develop and validate psirc, a computational method for identifying full-length circRNA isoforms and quantifying their expression from RNA sequencing data.
  • To investigate the differential expression of circRNA isoforms in nasopharyngeal carcinoma (NPC).

Main Methods:

  • Development of psirc, a bioinformatics tool for circRNA isoform identification and quantification.
  • Validation of psirc using simulated and experimental RNA sequencing data.
  • Application of psirc to transcriptome profiles of NPC and normal nasopharynx samples.

Main Results:

  • psirc effectively identifies full-length circRNA isoforms and quantifies their expression levels with computational efficiency.
  • Discovery and validation of circRNA isoforms differentially expressed between NPC and normal tissues.
  • Identification of alternatively spliced circRNA isoforms with up to 100-fold higher expression and fewer miRNA response elements compared to linear transcript-derived isoforms.

Conclusions:

  • Quantifying full-length circRNA isoforms is crucial for understanding their function and role in diseases like cancer.
  • psirc provides a robust method for comprehensive circRNA isoform analysis.
  • The findings highlight the significance of alternatively spliced circRNAs in nasopharyngeal carcinoma.