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Updated: Jul 16, 2025

Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within
Maya Suzuki1, Satoshi Sakai1, Kosuke Ota1
1Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, 431-3192, Japan.
CCIVR2 identifies antisense transcripts from divergent and convergent transcription. This bioinformatics tool reveals species-specific features and functional transcript pairs involved in biological processes.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
- Transcriptomics
Background:
- Divergent and convergent transcription involve adjacent sense and antisense transcripts.
- Structural characteristics of these transcriptions across species and RNA biotypes are not well understood.
Purpose of the Study:
- To develop a computational tool for identifying antisense transcripts from divergent/convergent transcription.
- To characterize the features of divergent/convergent transcription across multiple species and RNA biotypes.
Main Methods:
- Development of CCIVR2, a program to identify overlapping and non-overlapping antisense transcripts.
- Analysis of divergent/convergent transcription using CCIVR2 in 11 species.
- Identification of transcription start sites (TSS) and transcript end sites (TES) within specified regions.
Main Results:
- CCIVR2 successfully identified sense/antisense transcript pairs from divergent transcription.
- Species- and RNA biotype-specific features of divergent/convergent transcription were discovered.
- Functional transcript pairs involved in embryonic stem cell differentiation and TGFβ stimulation were identified.
Conclusions:
- CCIVR2 is a valuable bioinformatics tool for characterizing divergent/convergent transcription.
- The tool aids in identifying functional sense/antisense transcript pairs in specific biological contexts.
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