CircRNA—Protein Interactions in Muscle Development and Diseases

Zheng, Shuailong; Zhang, Xujia; Odame, Emmanuel; Xu, Xiaoli; Chen, Yuan; Ye, Jiangfeng; Zhou, Helin; Dai, Dinghui; Kyei, Bismark; Zhan, Siyuan; Cao, Jiaxue; Guo, Jiazhong; Zhong, Tao; Wang, Linjie; Li, Li; Zhang, Hongping

doi:10.3390/ijms22063262

Cited by 44 publications

(30 citation statements)

References 112 publications

(102 reference statements)

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“…They are rather more stable in comparison with their linear counterparts due to their resistance to ribonuclease (RNase) activities 25 . Circular RNAs have been proposed to function by means of miRNA sponging 26 , 27 , regulating transcription 28 , 29 and interacting with RNA-binding proteins (RBPs) 14 , 18 , 30 , 31 . Genome wide analysis has also demonstrated that circRNAs are evolutionary conserved among species 32 , 33 .…”

Section: Regulation Of Hippo-yap Signaling Axis By Circrnasmentioning

confidence: 99%

“…Owing to their covalently closed structure and restricted degradation by exonucleases, circRNAs have been observed to be more stable in comparison to their linear counterparts 14 . Generally, circRNA biogenesis is either mediated through alternative back-splicing 13 , lariat-driven mechanisms 15 , intron pairing-based circularization 16 , or circularization that follows pairing with RBPs (RNA Binding Proteins) 17 , 18 .…”

Section: Introductionmentioning

confidence: 99%

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Circular RNAs modulate Hippo-YAP signaling: functional mechanisms in cancer

Qadir¹,

Li²,

Yang³

2022

Theranostics

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The Hippo signaling pathway is an evolutionarily conserved network that regulates organ size and tissue homeostasis in mammals. This pathway controls various cell functions, such as growth, proliferation, survival, apoptosis, and stemness by switching 'on' or 'off' its inhibitory and/or transcriptional module, thereby regulating target gene(s) expression. Altered Hippo signaling has been implicated in various forms of cancers. Increasing evidence suggests cross-talk between the Hippo signaling pathway and non-coding RNAs, in particular circular RNAs (circRNAs). In this context, the current review presents the mechanistic interplay between the Hippo pathway and related circRNAs in various forms of cancers, along with the capabilities of these circRNAs to function either as tumor suppressors or oncogenes through miRNA sponging or protein binding mechanisms. Furthermore, we discuss the constraints and limitations in circRNA mechanistic studies while highlighting some outstanding questions regarding the roles of circRNAs associated with the Hippo-YAP pathway in cancer. Finally, we delineate the potential of these circRNAs to be employed as diagnostic and prognostic biomarkers, as well as molecular hotspots for cancer therapy.

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Section: Regulation Of Hippo-yap Signaling Axis By Circrnasmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Circular RNAs modulate Hippo-YAP signaling: functional mechanisms in cancer

Qadir¹,

Li²,

Yang³

2022

Theranostics

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“…CircRNAs are generated by the back-splicing of exonic, intronic, or intergenic regions. With the advance of high-throughput RNA sequencing (RNA-seq) technology, circRNAs were shown to be produced from thousands of loci in eukaryotes, from plants, animals to human beings [ 8 , 9 ], and were demonstrated to participate in multiple biological processes [ 10 , 11 ]. In recent years, they have been found to contribute substantially to host–virus interactions, specifically participating in the process of viral infection and the antiviral immune response.…”

Section: Introductionmentioning

confidence: 99%

RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus

Chen

Tian

et al. 2022

Animals

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H5N1, a highly pathogenic avian influenza virus that is prevalent in Asia, seriously harms the poultry industry and global public health. However, its pathogenesis is still not well understood. Circular RNAs (circRNAs), a newly identified type of RNA, reportedly play crucial roles in various pathogenic processes. In this study, RNA sequencing was performed to analyze the expression profile of circRNAs in H5N1-infected chicken embryo fibroblast (DF1) cells. A total of 14,586 circRNAs were identified. The expression profiles of infected cells changed more significantly, relative to uninfected cells, as the infection period was extended; namely, 261, 626, and 1103 circRNAs exhibited differential expression in cells infected for 6 h, 12 h, and 20 h, respectively. GO and KEGG enrichment analysis revealed significant enrichment of the parental genes of the differentially expressed circRNAs for viral replication and immune response-related pathways, such as positive regulation of transcription from the RNA polymerase II promoter, positive regulation of I-kappaB kinase/NF-kappaB signaling, innate immune response, and ubiquitin protein ligase activity. In conclusion, we identified the expression profile of circRNAs in H5N1-infected chicken DF1 cells. Bioinformatic analyses of the dysregulated circRNAs suggest that circRNAs might play important roles in the pathogenesis of H5N1 infection, offering new insights into the mechanisms underlying H5N1–host interaction.

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“…Hansen et al found that exonic circRNA CDR1as can bind with miR-671, which can degrade CDR1as mediated by AGO ( Hansen et al, 2013 ), and the binding sites are highly conserved. In addition, circRNAs can also interact with RNA binding proteins as endogenous competitive RNA (S. Zheng et al, 2021 ). The gene muscleblind ( MBL ) of Drosophila can encode MBL protein as a transcript factor, and MBL regulates the dynamic balance of circular transcript (circRNA circMbl) and linear transcript ( Ashwal-Fluss et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of CircRNA Sequence Assembly Methods Using Long Reads

et al. 2022

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The functional study on circRNAs has been increasing in the past decade due to its important roles in micro RNA sponge, protein coding, the initiation, and progression of diseases. The study of circRNA functions depends on the full-length sequences of circRNA, and current sequence assembly methods based on short reads face challenges due to the existence of linear transcript. Long reads produced by long-read sequencing techniques such as Nanopore technology can cover full-length sequences of circRNA and therefore can be used to evaluate the correctness and completeness of circRNA full sequences assembled from short reads of the same sample. Using long reads of the same samples, one from human and the other from mouse, we have comprehensively evaluated the performance of several well-known circRNA sequence assembly algorithms based on short reads, including circseq_cup, CIRI_full, and CircAST. Based on the F1 score, the performance of CIRI-full was better in human datasets, whereas in mouse datasets CircAST was better. In general, each algorithm was developed to handle special situations or circumstances. Our results indicated that no single assembly algorithm generated better performance in all cases. Therefore, these assembly algorithms should be used together for reliable full-length circRNA sequence reconstruction. After analyzing the results, we have introduced a screening protocol that selects out exonic circRNAs with full-length sequences consisting of all exons between back splice sites as the final result. After screening, CIRI-full showed better performance for both human and mouse datasets. The average F1 score of CIRI-full over four circRNA identification algorithms increased from 0.4788 to 0.5069 in human datasets, and it increased from 0.2995 to 0.4223 in mouse datasets.

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CircRNA—Protein Interactions in Muscle Development and Diseases

Cited by 44 publications

References 112 publications

Circular RNAs modulate Hippo-YAP signaling: functional mechanisms in cancer

Circular RNAs modulate Hippo-YAP signaling: functional mechanisms in cancer

RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus

Evaluation of CircRNA Sequence Assembly Methods Using Long Reads

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