Specific identification and quantification of circular RNAs from sequencing data

Cheng, Jianghua; Metge, Franziska; Dieterich, Christoph

doi:10.1093/bioinformatics/btv656

Cited by 320 publications

(297 citation statements)

References 7 publications

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“…The DCC software [10] was used to identify circRNA candidates from chimeric read mappings (see Materials and Methods). This initial step yielded 8375 potential circRNA regions.…”

Section: Resultsmentioning

confidence: 99%

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Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts

Jakobi

Czaja-Hasse²,

Reinhardt³

et al. 2016

Genomics, Proteomics &Amp; Bioinformatics

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For several decades, cardiovascular disease has been the leading cause of death throughout all countries. There is a strong genetic component to many disease subtypes (e.g., cardiomyopathy) and we are just beginning to understand the relevant genetic factors. Several studies have related RNA splicing to cardiovascular disease and circular RNAs (circRNAs) are an emerging player. circRNAs, which originate through back-splicing events from primary transcripts, are resistant to exonucleases and typically not polyadenylated. Initial functional studies show clear phenotypic outcomes for selected circRNAs. We provide, for the first time, a comprehensive catalogue of RNase R-resistant circRNA species for the adult murine heart. This work combines state-of-the-art circle sequencing with our novel DCC software to explore the circRNA landscape of heart tissue. Overall, we identified 575 circRNA species that pass a beta-binomial test for enrichment (false discovery rate of 1%) in the exonuclease-treated sequencing sample. Several circRNAs can be directly attributed to host genes that have been previously described as associated with cardiovascular disease. Further studies of these candidate circRNAs may reveal disease-relevant properties or functions of specific circRNAs.

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“…The DCC software [10] was used to identify circRNA candidates from chimeric read mappings (see Materials and Methods). This initial step yielded 8375 potential circRNA regions.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, we recently presented a statistical framework to detect host gene-independent circRNA expression changes from sequencing data [10].…”

Section: Introductionmentioning

confidence: 99%

Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts

Jakobi

Czaja-Hasse²,

Reinhardt³

et al. 2016

Genomics, Proteomics &Amp; Bioinformatics

Self Cite

View full text Add to dashboard Cite

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“…After 3′ adapter trimming and low-quality read removal with cutadapt software (v1.9.3), high-quality reads were aligned to the reference genome/transcriptome with STAR software [14]. circRNAs were detected and annotated with DCC software [15] using two public circRNA databases: circBase [16] and circ2Traits [17]. The junction read counts were normalized, and differentially expressed circRNAs were determined using the edgeR package of R software [18].…”

Section: Patient Samplesmentioning

confidence: 99%

The Landscape of Circular RNA Expression Profiles in Papillary Thyroid Carcinoma Based on RNA Sequencing

Lan

Chen

et al. 2018

Cell Physiol Biochem

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Background/Aims: Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. However, the molecular mechanisms responsible for its tumorigenesis and progression remain largely unknown. Circular RNA (circRNA) is a novel type of noncoding RNA that can serve as an ideal biomarker due to its stability. Recent evidence suggests that circRNAs play important roles in tumorigenesis. This study aims to investigate circRNA expression profiles and their potential biological functions in PTC. Methods: High-throughput RNA sequencing was used to assess circRNA expression profiles in PTC, and quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate dysregulated circRNAs. Receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic value of circRNAs for PTC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to determine the biological functions of differentially expressed circRNAs. Bioinformatic analyses were applied to predict interactions between circRNAs and microRNAs (miRNAs), and a circRNA-miRNA-mRNA network was constructed using Cytoscape software. Results: We identified a number of differentially expressed circRNAs in PTC tissues compared with paired normal thyroid tissues, with chr5: 160757890-160763776–, chr12: 40696591-40697936+, chr7: 22330794-22357656-, and chr21: 16386665-16415895– being upregulated, and chr7: 91924203-91957214+, chr2: 179514891-179516047–, chr9: 16435553-16437522–, and chr22: 36006931-36007153– being downregulated. These findings were confirmed by qRT-PCR, and ROC curves indicated that they can serve as potential biomarkers for PTC. GO and KEGG pathway analyses showed that some of these circRNAs are related to cancers. Additionally, bioinformatic analyses revealed a potential competing-endogenous-RNA-regulating network among circRNAs, miRNAs, and mRNAs. Conclusions: Our study results depict the landscape of circRNA expression profiles in PTC and also provide potential biomarkers for PTC. Further functional and mechanistic studies of these circRNAs may improve our understanding of PTC tumorigenesis.

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“…The resulting high-quality trimmed reads were used to analyze circRNA. The high-quality reads were aligned to the reference genome/ transcriptome using STAR [29] software and circRNAs were identified using DCC [30] software and annotated from the circBase [31] database.…”

Section: Sequencing Analysis Of Circrnamentioning

confidence: 99%

Identification of Circular RNAs Altered in Mouse Jejuna After Radiation

Lu¹,

Gong²,

Wang³

et al. 2018

Cell Physiol Biochem

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Background/Aims: Circular RNAs (circRNAs) make up a large class of non-coding RNAs and play important roles in a variety of diseases, including nervous system diseases and cancers. The intestinal epithelium is sensitive to ionizing radiation, radiotherapy of abdominal or pelvic tumors or nuclear accident exposure can lead to high radiation toxicity, which can result in radiation-induced intestinal injury. The goal of this present study was to analyze the potential roles of circRNAs in radiation-induced intestinal injury. Methods: Mice were divided into two groups: control group and irradiated group. Irradiated group was 3.5 days after 14Gy abdominal irradiation (ABI) group. We started with RNA-seq of circRNA changes in mouse jejuna after radiation and validated by RT-PCR in the following experimental. miRNAs targeted mRNAs were predicted using proprietary software based on target scan and Miranda. The network of circRNA-miRNA-mRNA was illustrated by cytoscape software. Results: 2751 circRNAs were detected in the two groups. At day 3.5 post-radiation, 42 and 48 circRNAs were found to be significantly upregulated and downregulated, respectively, compared to the control (p≤0.05, Fold Change ≥2). Further, the altered expression of 10 circRNAs (chr18: 35610871-35613502+, chr15: 95864225-95894541+, chr3: 96041338-96042928-, chr5: 64096979-64108263+, chr19: 16705875-16710941-, chr5: 134491893-134500149-, chr19: 42562552-42564341+, chr5: 32640331-32664400+, chr3: 72958113-72960367- and chr8: 79343654-79372364-) were verified by RT-PCR. Compared the miRNA-targeted mRNAs with our mRNAs sequencing data, we found 14 upregulated circRNA-targeted mRNAs were also unregulated and 22 downregulated circRNAs-targeted mRNAs were also downregulated. Gene ontology and KEGG pathway analyses indicated the predicted genes were mainly involved in the MAPK signaling pathway. Conclusions: This study reveals that expression of circRNAs was altered in the jejuna of mice post-irradiation and provides a resource for the study of circRNAs in radiation-induced intestinal injury and repair.

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Specific identification and quantification of circular RNAs from sequencing data

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 320 publications

References 7 publications

Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts

Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts

The Landscape of Circular RNA Expression Profiles in Papillary Thyroid Carcinoma Based on RNA Sequencing

Identification of Circular RNAs Altered in Mouse Jejuna After Radiation

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