CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

Ma, Xu-Kai; Wang, Meng-Ran; Liu, Chu-Xiao; Dong, Rui; Carmichael, Gordon G.; Chen, Lingling; Yang, Li

doi:10.1016/j.gpb.2019.11.004

Cited by 65 publications

(68 citation statements)

References 30 publications

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“…To identify the expression of circRNAs from RNA-Seq, one extensively used algorithm Circexplorer3 [43] were utilized for detecting the back-splice junction sites of circRNAs. And the fragments per billion mapped bases (FPB) of circRNA and its linear host gene were extracted to calculate the CIRCscore (FPBcirc/FPBlinear), which could indicate the expression ratio of circRNA to their host genes.…”

Section: Identification Of Circrna Expressionmentioning

confidence: 99%

CircRNA inhibits DNA damage repair by interacting with host gene

et al. 2020

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Background: Deregulated circular RNAs (circRNAs) are associated with the development of cancer and therapy resistance. However, functional research of circRNAs mostly focus on potential miRNA or protein binding and more potential regulation of circRNA on host gene DNA in cancers are yet to be inspected. Method: We performed total RNA sequencing on clinical breast cancer samples and identified the expression patterns of circRNAs and corresponding host genes in patient blood, tumor and adjacent normal tissues. qPCR, northern blot and in situ hybridization were used to validate the dysregulation of circRNA circSMARCA5. A series of procedures including R-loop dot-blotting, DNA-RNA immunoprecipitation and mass spectrum, etc. were conducted to explore the regulation of circSMARCA5 on the transcription of exon 15 of SMARCA5. Moreover, immunofluorescence and in vivo experiments were executed to investigate the overexpression of circSMARCA5 with drug sensitivities. Results: We found that circRNAs has average higher expression over its host linear genes in peripheral blood. Compared to adjacent normal tissues, circSMARCA5 is decreased in breast cancer tissues, contrary to host gene SMARCA5. The enforced expression of circSMARCA5 induced drug sensitivity of breast cancer cell lines in vitro and in vivo. Furthermore, we demonstrated that circSMARCA5 can bind to its parent gene locus, forming an R-loop, which results in transcriptional pausing at exon 15 of SMARCA5. CircSMARCA5 expression resulted in the downregulation of SMARCA5 and the production of a truncated nonfunctional protein, and the overexpression of circSMARCA5 was sufficient to improve sensitivity to cytotoxic drugs. Conclusion: Our results revealed a new regulatory mechanism for circRNA on its host gene and provided evidence that circSMARCA5 may serve as a therapeutic target for drug-resistant breast cancer patients.

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Section: Identification Of Circrna Expressionmentioning

confidence: 99%

CircRNA inhibits DNA damage repair by interacting with host gene

et al. 2020

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“…We also attempted to detect circRNAs by existing tools. However, tools such as circRNAfinder ( https://github.com/bioxfu/circRNAFinder ) und CIRCexplorer [ 40 ] were not feasible, since they rely on annotation of eukaryotic splicing events. For de novo identification of circRNA candidates, we used CIRI2 [ 41 ].…”

Section: Resultsmentioning

confidence: 99%

iCLIP analysis of RNA substrates of the archaeal exosome

et al. 2020

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Background The archaeal exosome is an exoribonucleolytic multiprotein complex, which degrades single-stranded RNA in 3′ to 5′ direction phosphorolytically. In a reverse reaction, it can add A-rich tails to the 3′-end of RNA. The catalytic center of the exosome is in the aRrp41 subunit of its hexameric core. Its RNA-binding subunits aRrp4 and aDnaG confer poly(A) preference to the complex. The archaeal exosome was intensely characterized in vitro, but still little is known about its interaction with natural substrates in the cell, particularly because analysis of the transcriptome-wide interaction of an exoribonuclease with RNA is challenging. Results To determine binding sites of the exosome to RNA on a global scale, we performed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) analysis with antibodies directed against aRrp4 and aRrp41 of the chrenarchaeon Sulfolobus solfataricus. A relatively high proportion (17–19%) of the obtained cDNA reads could not be mapped to the genome. Instead, they corresponded to adenine-rich RNA tails, which are post-transcriptionally synthesized by the exosome, and to circular RNAs (circRNAs). We identified novel circRNAs corresponding to 5′ parts of two homologous, transposase-related mRNAs. To detect preferred substrates of the exosome, the iCLIP reads were compared to the transcript abundance using RNA-Seq data. Among the strongly enriched exosome substrates were RNAs antisense to tRNAs, overlapping 3′-UTRs and RNAs containing poly(A) stretches. The majority of the read counts and crosslink sites mapped in mRNAs. Furthermore, unexpected crosslink sites clustering at 5′-ends of RNAs was detected. Conclusions In this study, RNA targets of an exoribonuclease were analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes, and underlines its role in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5′-ends of genes suggests simultaneous binding of both RNA ends by the S. solfataricus exosome. This may serve to prevent translation of mRNAs dedicated to degradation in 3′-5′ direction.

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“…CIRCexplorer2 ( Zhang et al, 2016 ) and CLEAR/CIRCexplorer3 ( Ma et al, 2019 ) were mainly used to obtain circRNAs in our research. For CIRCexplorer2, we used the parse module to analyze circRNA fusion junction reads and annotate modules for circRNA gene information.…”

Section: Methodsmentioning

confidence: 99%

Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer

Zhang

et al. 2021

Front. Genet.

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Prostate cancer (PCa) is the most common malignant tumor in men, and its incidence increases with age. Serum prostate-specific antigen and tissue biopsy remain the standard for diagnosis of suspected PCa. However, these clinical indicators may lead to aggressive overtreatment in patients who have been treated sufficiently with active surveillance. Circular RNAs (circRNAs) have been recently recognized as a new type of regulatory RNA that is not easily degraded by RNases and other exonucleases because of their covalent closed cyclic structure. Thus, we utilized high-throughput sequencing data and bioinformatics analysis to identify specifically expressed circRNAs in PCa and filtered out five specific circRNAs for further analysis—hsa_circ_0006410, hsa_circ_0003970, hsa_circ_0006754, hsa_circ_0005848, and a novel circRNA, hsa_circ_AKAP7. We constructed a circRNA-miRNA regulatory network and used miRNA and differentially expressed mRNA interactions to predict the function of the selected circRNAs. Furthermore, survival analysis of their cognate genes and PCR verification of these five circRNAs revealed that they are closely related to well-known PCa pathways such as the MAPK signaling pathway, P53 pathway, androgen receptor signaling pathway, cell cycle, hormone-mediated signaling pathway, and cellular lipid metabolic process. By understanding the related metabolism of circRNAs, these circRNAs could act as metabolic biomarkers, and monitoring their levels could help diagnose PCa. Meanwhile, the exact regulatory mechanism for AR-related regulation in PCa is still unclear. The circRNAs we found can provide new solutions for research in this field.

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CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

Cited by 65 publications

References 30 publications

CircRNA inhibits DNA damage repair by interacting with host gene

CircRNA inhibits DNA damage repair by interacting with host gene

iCLIP analysis of RNA substrates of the archaeal exosome

Five Circular RNAs in Metabolism Pathways Related to Prostate Cancer

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