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Updated: Aug 1, 2026
Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq
Isabel S Naarmann-de Vries1,2, Jessica Eschenbach1, Sarah Schudy2,3
1Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany.
Abstract:
Recently, circular RNAs (circRNAs) have been extensively studied in animals and plants. circRNAs are generated by backsplicing from the same linear transcripts that are canonically spliced to produce, for example, mature mRNAs. circRNAs exhibit tissue-specific expression and are potentially involved in many diseases, among them cardiovascular diseases. The comprehensive analysis of circRNA expression patterns across larger patient cohorts requires a streamlined and cost-effective workflow designed to meet small input requirements. In this article, we present Lexo-circSeq, a targeted RNA sequencing approach that can profile up to 110 circRNAs and their corresponding linear transcripts in one experiment. We established Lexo-circSeq employing total human heart RNA and show that our protocol can detect depletion of a specific circRNA in hiPSC-derived cardiomyocytes. Finally, Lexo-circSeq was applied to biopsies from patients diagnosed with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), respectively. Interestingly, our results indicate that circular-to-linear-ratios for circSLC8A1 and circRBM33 are deregulated in cardiomyopathy.
Insights
Lexo-circSeq is a novel RNA sequencing method for profiling circular RNAs (circRNAs) and linear transcripts. This approach identified deregulated circular-to-linear ratios in cardiomyopathy patients.
Area of Science:
- Molecular Biology
- Genomics
- Cardiovascular Research
Background:
- Circular RNAs (circRNAs) are increasingly recognized for their roles in biological processes.
- Their involvement in diseases, including cardiovascular conditions, necessitates efficient expression analysis.
- Existing methods often require substantial RNA input, limiting large-scale patient cohort studies.
Purpose of the Study:
- To develop a streamlined, cost-effective targeted RNA sequencing workflow for profiling circRNAs and their linear counterparts.
- To validate the workflow's sensitivity using human heart RNA and induced pluripotent stem cell-derived cardiomyocytes.
- To investigate circRNA expression patterns in patients with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM).
Main Methods:
- Development of Lexo-circSeq, a targeted RNA sequencing approach.
- Profiling up to 110 specific circRNAs and their cognate linear transcripts simultaneously.
- Application of the protocol to human heart RNA, hiPSC-derived cardiomyocytes, and patient biopsies from DCM and HCM cohorts.
Main Results:
- Lexo-circSeq successfully profiled circRNAs and linear transcripts from limited human heart RNA samples.
- The method detected circRNA depletion in hiPSC-derived cardiomyocytes.
- Analysis of cardiomyopathy patient biopsies revealed deregulated circular-to-linear ratios for circSLC8A1 and circRBM33.
Conclusions:
- Lexo-circSeq offers a sensitive and efficient method for analyzing circRNA and linear transcript expression.
- This targeted sequencing approach is suitable for large patient cohorts and limited sample inputs.
- Aberrant circular-to-linear ratios of specific circRNAs may serve as potential biomarkers for cardiomyopathies.
