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Updated: Nov 21, 2025

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

isoCirc catalogs full-length circular RNA isoforms in human transcriptomes.

Ruijiao Xin¹, Yan Gao^1,2, Yuan Gao¹

¹Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.

Nature Communications

|January 13, 2021

Summary

This summary is machine-generated.

We developed isoCirc, a new method to sequence full-length circular RNAs (circRNAs). This approach overcomes short-read limitations, enabling comprehensive circRNA isoform cataloging and the discovery of novel splicing events in human tissues.

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Last Updated: Nov 21, 2025

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

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

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

Published on: October 21, 2022

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Circular RNAs (circRNAs) are a significant class of functional RNA molecules.
Short-read RNA sequencing (RNA-seq) is a common method for circRNA identification but cannot determine full-length sequences or precise exonic compositions.
Limitations in current sequencing technologies hinder a complete understanding of circRNA diversity and function.

Purpose of the Study:

To introduce isoCirc, a novel strategy for sequencing full-length circular RNA (circRNA) isoforms.
To establish an integrated computational pipeline for reliable characterization of circRNA isoforms from isoCirc data.
To generate a comprehensive catalog of human circRNA isoforms and identify novel splicing events.

Main Methods:

Developed isoCirc, a strategy combining rolling circle amplification with nanopore long-read sequencing to capture full-length circRNA isoforms.
Created an integrated computational pipeline for analyzing isoCirc data and characterizing circRNA isoforms.
Applied isoCirc to 12 human tissues and one human cell line (HEK293) to generate a circRNA catalog.

Main Results:

Generated a comprehensive catalog of 107,147 full-length circRNA isoforms, including 40,628 isoforms of 500 nt or longer.
Identified widespread alternative splicing events within circRNAs, notably 720 retained intron events.
Discovered a class of exon-intron circRNAs (EIciRNAs) characterized by retained introns.

Conclusions:

The isoCirc strategy effectively sequences full-length circRNA isoforms, overcoming limitations of short-read sequencing.
The generated dataset provides a valuable resource for studying the complexity of circRNAs in the human transcriptome.
This work enhances the understanding of circRNA diversity, including novel splicing patterns like EIciRNAs.