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Identification of Circular RNAs using RNA Sequencing
Published on: November 14, 2019
Expression profiling of circular RNAs and their potential role in early‑stage diabetic cardiomyopathy
Shengzhong Dong1, Chunyan Tu1, Xing Ye1
1Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R. China.
Insights
Early detection of diabetic cardiomyopathy (DCM) is challenging. This study identifies novel circular RNAs (circRNAs) in early-stage DCM in mice, revealing potential biomarkers and therapeutic targets for this diabetes mellitus complication.
Area of Science:
- Cardiovascular Research
- Molecular Biology
- Genomics
Background:
- Diabetic cardiomyopathy (DCM) is a serious complication of diabetes mellitus (DM).
- Early detection of DCM is difficult due to poorly understood molecular mechanisms.
- Circular RNAs (circRNAs) are implicated in various diseases, but their role in early DCM is unclear.
Purpose of the Study:
- To investigate the role of circRNAs in the early stages of diabetic cardiomyopathy.
- To identify differentially expressed circRNAs in a mouse model of DCM.
- To elucidate potential circRNA-miRNA-mRNA regulatory networks in early DCM.
Main Methods:
- High-throughput RNA sequencing of heart tissues from BKS-db/db mice.
- Reverse transcription-quantitative PCR for circRNA validation.
- Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis.
- Prediction and verification of circRNA-miRNA-mRNA interactions.
Main Results:
- Identified 58 significantly differentially expressed circRNAs in db/db mice.
- Validated six upregulated and seven downregulated circRNAs.
- Discovered five circRNAs acting as competing endogenous RNAs (ceRNAs) in DCM.
- Determined two potential circRNA-miRNA-mRNA regulatory networks.
- Suggested mmu_circ_0001160 may encode a protein.
Conclusions:
- This study provides a comprehensive circRNA expression profile in early DCM.
- Identified novel circRNA-miRNA-mRNA networks offer insights into DCM pathogenesis.
- These findings highlight potential biomarkers and therapeutic targets for early-stage DCM treatment.
Abstract:
Diabetic cardiomyopathy (DCM) is a severe cardiovascular complication of diabetes mellitus (DM). Detecting DCM during the early stages of the disease remains a challenge, as the molecular mechanisms underlying early‑stage DCM are not clearly understood. Circular RNA (circRNA), a type of non‑coding RNA, has been confirmed to be associated with numerous diseases. However, it is still unclear how circRNAs are involved in early‑stage DCM. In the present study, heart tissues harvested from BKS‑db/db knock‑out mice were identified through high‑throughput RNA sequencing technology. A total of 58 significantly differentially expressed circRNAs were identified in the db/db sample. Among these, six upregulated circRNAs and seven downregulated circRNAs were detected by reverse transcription‑quantitative PCR and analyzed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Furthermore, based on the predicted binding site with microRNAs (miRNAs) involved in DCM, five circRNAs (mmu_circ_0000652, mmu_circ_0000547, mmu_circ_0001058, mmu_circ_0000680 and novel_circ_0004285) were shown to serve as competing endogenous (ce)RNAs. The corresponding miRNAs and mRNAs of the ceRNAs were also verified, and two promising circRNA‑miRNA‑mRNA regulatory networks were determined. Finally, internal ribosome entry site prediction combined with open reading frame prediction indicated that it was highly possible that mmu_circ_0001160 encoded a protein. In the present study, a comprehensive analysis of the circRNA expression profile during the early phase of DCM was performed, and two promising circRNA‑miRNA‑mRNA regulatory networks were identified. These results lay the foundation for unravelling the underlying pathogenesis of DCM, and highlight potential biomarkers and therapeutic targets for the treatment of DCM at an early stage.
