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Ren Y, Li J, Liu J, Zhang Z, Song Y, Fan D, Liu M, Zhang L, Xu Y, Guo D, He J, Song S, Gao Z, Ma C. Functional Differences of Grapevine Circular RNA Vv-circPTCD1 in Arabidopsis and Grapevine Callus under Abiotic Stress. Plants (Basel) 2023; 12:2332. [PMID: 37375960 DOI: 10.3390/plants12122332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Circular RNAs (circRNAs) serve as covalently closed single-stranded RNAs and have been proposed to influence plant development and stress resistance. Grapevine is one of the most economically valuable fruit crops cultivated worldwide and is threatened by various abiotic stresses. Herein, we reported that a circRNA (Vv-circPTCD1) processed from the second exon of the pentatricopeptide repeat family gene PTCD1 was preferentially expressed in leaves and responded to salt and drought but not heat stress in grapevine. Additionally, the second exon sequence of PTCD1 was highly conserved, but the biogenesis of Vv-circPTCD1 is species-dependent in plants. It was further found that the overexpressed Vv-circPTCD1 can slightly decrease the abundance of the cognate host gene, and the neighboring genes are barely affected in the grapevine callus. Furthermore, we also successfully overexpressed the Vv-circPTCD1 and found that the Vv-circPTCD1 deteriorated the growth during heat, salt, and drought stresses in Arabidopsis. However, the biological effects on grapevine callus were not always consistent with those of Arabidopsis. Interestingly, we found that the transgenic plants of linear counterpart sequence also conferred the same phenotypes as those of circRNA during the three stress conditions, no matter what species it is. Those results imply that although the sequences are conserved, the biogenesis and functions of Vv-circPTCD1 are species-dependent. Our results indicate that the plant circRNA function investigation should be conducted in homologous species, which supports a valuable reference for further plant circRNA studies.
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Affiliation(s)
- Yi Ren
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junpeng Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingjing Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
| | - Zhen Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Song
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongying Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Minying Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lipeng Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
| | - Yuanyuan Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dinghan Guo
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan He
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiren Song
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhen Gao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Chao Ma
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Colantoni A, Capauto D, Alfano V, D'Ambra E, D'Uva S, Tartaglia GG, Morlando M. FUS Alters circRNA Metabolism in Human Motor Neurons Carrying the ALS-Linked P525L Mutation. Int J Mol Sci 2023; 24. [PMID: 36834591 DOI: 10.3390/ijms24043181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Deregulation of RNA metabolism has emerged as one of the key events leading to the degeneration of motor neurons (MNs) in Amyotrophic Lateral Sclerosis (ALS) disease. Indeed, mutations on RNA-binding proteins (RBPs) or on proteins involved in aspects of RNA metabolism account for the majority of familiar forms of ALS. In particular, the impact of the ALS-linked mutations of the RBP FUS on many aspects of RNA-related processes has been vastly investigated. FUS plays a pivotal role in splicing regulation and its mutations severely alter the exon composition of transcripts coding for proteins involved in neurogenesis, axon guidance, and synaptic activity. In this study, by using in vitro-derived human MNs, we investigate the effect of the P525L FUS mutation on non-canonical splicing events that leads to the formation of circular RNAs (circRNAs). We observed altered levels of circRNAs in FUSP525L MNs and a preferential binding of the mutant protein to introns flanking downregulated circRNAs and containing inverted Alu repeats. For a subset of circRNAs, FUSP525L also impacts their nuclear/cytoplasmic partitioning, confirming its involvement in different processes of RNA metabolism. Finally, we assess the potential of cytoplasmic circRNAs to act as miRNA sponges, with possible implications in ALS pathogenesis.
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3
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Wang W, Sun L, Huang MT, Quan Y, Jiang T, Miao Z, Zhang Q. Regulatory circular RNAs in viral diseases: applications in diagnosis and therapy. RNA Biol 2023; 20:847-858. [PMID: 37882652 PMCID: PMC10730172 DOI: 10.1080/15476286.2023.2272118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
Circular RNA (circRNA) forms closed loops via back-splicing in precursor mRNA, resisting exonuclease degradation. In higher eukaryotes, protein-coding genes create circRNAs through exon back-splicing. Unlike mRNAs, circRNAs possess unique production and structural traits, bestowing distinct cellular functions and biomedical potential. In this review, we explore the pivotal roles of viral circRNAs and associated RNA in various biological processes. Analysing the interactions between viral circRNA and host cellular machinery yields fresh insights into antiviral immunity, catalysing the development of potential therapeutics. Furthermore, circRNAs serve as enduring biomarkers in viral diseases due to their stable translation within specific tissues. Additionally, a deeper understanding of translational circRNA could expedite the establishment of circRNA-based expression platforms, meeting the rising demand for broad-spectrum viral vaccines. We also highlight the applications of circular RNA in biomarker studies as well as circRNA-based therapeutics. Prospectively, we expect a technological revolution in combating viral infections using circRNA.
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Affiliation(s)
- Wei Wang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Lei Sun
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Meng-Ting Huang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun Quan
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Zhichao Miao
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qiong Zhang
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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4
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Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE, Yang L, Zhao F. A guide to naming eukaryotic circular RNAs. Nat Cell Biol 2023; 25:1-5. [PMID: 36658223 PMCID: PMC10114414 DOI: 10.1038/s41556-022-01066-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Alternative splicing of eukaryotic transcripts often leads to production of multiple mature RNAs from a single gene locus. In addition to encoding linear RNAs, genes can produce stable circular RNAs (circRNAs) that are often co-expressed with their cognate linear RNAs. Multiple distinct circRNAs are frequently generated from a gene locus via back-splicing, with each mature transcript having a potentially unique function due to its distinct combination of exons and sometimes retained introns. However, names currently given to circRNAs are often ambiguous and lack consistency across studies. Here, we call on the community to embrace standards for naming circRNAs so that a common nomenclature is used to ensure clarity and reproducibility.
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Affiliation(s)
- Ling-Ling Chen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Albrecht Bindereif
- Institute of Biochemistry, Faculty of Biology and Chemistry, Justus Liebig University of Giessen, Giessen, Germany
| | - Irene Bozzoni
- Department of Biology and Biotechnologies 'Charles Darwin' and IIT Center for Life Nano- & Neuro-Science@Sapienza, Sapienza University of Rome, Rome, Italy
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - A Gregory Matera
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Thomas B Hansen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, Singapore
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Hemholtz Association, Berlin, Germany
| | - Julia Salzman
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA.
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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5
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Yu L, Lobanov A, Zheng ZM. Reply to Wang et al., "Assessment of the Abundance and Potential Function of Human Papillomavirus Type 16 Circular E7 RNA". mBio 2022; 13:e0075822. [PMID: 35579355 DOI: 10.1128/mbio.00758-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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6
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Abstract
Most circular RNAs are produced from the back-splicing of exons of precursor mRNAs. Recent technological advances have in part overcome problems with their circular conformation and sequence overlap with linear cognate mRNAs, allowing a better understanding of their cellular roles. Depending on their localization and specific interactions with DNA, RNA, and proteins, circular RNAs can modulate transcription and splicing, regulate stability and translation of cytoplasmic mRNAs, interfere with signaling pathways, and serve as templates for translation in different biological and pathophysiological contexts. Emerging applications of RNA circles to interfere with cellular processes, modulate immune responses, and direct translation into proteins shed new light on biomedical research. In this review, we discuss approaches used in circular RNA studies and the current understanding of their regulatory roles and potential applications.
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Affiliation(s)
- Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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7
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Abstract
Circular RNA (circRNA) is a novel endogenous non-coding RNA (ncRNA) that, like microRNA (miRNA), is a rapidly emerging RNA research topic. CircRNA, unlike traditional linear RNAs (which have 5' and 3' ends), has a closed-loop structure that is unaffected by RNA exonucleases. Thus, circRNA has sustained expression and is less sensitive to degradation. Since circRNAs have many miRNAs binding sites, eliminating their repressive effects on their target genes can strongly enhance their expression. CircRNAs serve an important regulatory role in disease onset and progression via specific circRNA-miRNA interactions. We summarized the current progress in elucidating mechanisms and biogenesis of circRNAs in this review. In particular, circRNAs can function mainly as miRNA sponges, regulating host gene expression and protein transportation. Finally, we discussed the application prospects and significant challenges for the development of circRNA-based therapeutics.
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Affiliation(s)
- Xian Zhao
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Youxiu Zhong
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Xudong Wang
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Jiuheng Shen
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Wenlin An
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
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8
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Abstract
Ubiquitous in eukaryotes, circular RNAs (circRNAs) comprise a large class of mostly non-coding RNAs produced by back-splicing. Although some circRNAs have demonstrated biochemical activities, whether most circRNAs are functional is unknown. Here, we test the hypothesis that circRNA production primarily results from splicing error and so is deleterious instead of beneficial. In support of the error hypothesis, our analysis of RNA sequencing data from 11 shared tissues of humans, macaques, and mice finds that (1) back-splicing is much rarer than linear-splicing, (2) the rate of back-splicing diminishes with the splicing amount, (3) the overall prevalence of back-splicing in a species declines with its effective population size, and (4) circRNAs are overall evolutionarily unconserved. We estimate that more than 97% of the observed circRNA production is deleterious. We identify a small number of functional circRNA candidates, and the genome-wide trend strongly suggests that circRNAs are largely non-functional products of splicing errors.
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Affiliation(s)
- Chuan Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
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9
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Xu H, Fang MD, Li C, Liu C, Ren J, Zhang YM. [Progress in Research on the Novel Tumor Marker circRNA]. Zhongguo Yi Xue Ke Xue Yuan Xue Bao 2021; 43:435-444. [PMID: 34238421 DOI: 10.3881/j.issn.1000-503x.12920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Circular RNA(circRNA)is a novel type of endogenous non-coding RNA.Most circRNAs act as microRNA(miRNA)sponges to regulate the expression of functional genes.In addition,some circRNAs can be translated and interact with RNA-binding proteins to perform biological functions.The expression of circRNAs is prevalent in tissues and body fluids,and their abnormal expression is related to tumor progression.circRNAs are stable even under the treatment of RNase R because of their circular conformation.As circRNAs have construct stability,wide variety,specific regulation of tumor progression and high expression in body fluids,it is potential for circRNAs to serve as candidate diagnostic,prognostic and therapeutic targets.However,the knowledge about circRNAs remains poor.In addition to the not completely resolved functions and generation mechanisms of circRNAs,the annotations of circRNAs are also waiting for expanding.Here,we review the generation mechanisms,biological functions,and application of circRNAs in tumor research,aiming to provide integrated information for the future research.
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Affiliation(s)
- Hao Xu
- Center for Molecular Medicine,Hangzhou Medical College,Zhejiang Academy of Medical Sciences,Hangzhou 310013,China
| | - Meng-Die Fang
- Center for Molecular Medicine,Hangzhou Medical College,Zhejiang Academy of Medical Sciences,Hangzhou 310013,China
| | - Chao Li
- Center for Molecular Medicine,Hangzhou Medical College,Zhejiang Academy of Medical Sciences,Hangzhou 310013,China
| | - Chen Liu
- Center for Molecular Medicine,Hangzhou Medical College,Zhejiang Academy of Medical Sciences,Hangzhou 310013,China
| | - Juan Ren
- Center for Molecular Medicine,Hangzhou Medical College,Zhejiang Academy of Medical Sciences,Hangzhou 310013,China
| | - Yan-Mei Zhang
- Center for Molecular Medicine,Hangzhou Medical College,Zhejiang Academy of Medical Sciences,Hangzhou 310013,China
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10
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Qi Y, Han W, Chen D, Zhao J, Bai L, Huang F, Dai Z, Li G, Chen C, Zhang W, Zhang J, Jin B, Wang Y. Engineering circular RNA regulators to specifically promote circular RNA production. Theranostics 2021; 11:7322-7336. [PMID: 34158853 PMCID: PMC8210604 DOI: 10.7150/thno.56990] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/07/2021] [Indexed: 12/28/2022] Open
Abstract
Background: A large number of circular RNAs (circRNAs) have been discovered in the mammalian transcriptome with high abundance, which play vital roles in gene regulation, thereby participating in the development of multiple diseases. However, the biogenesis, regulation, and especially manipulation of circRNAs still remain largely unknown. Methods: Engineering circRNA regulators (ECRRs) were developed to promote circRNA biogenesis. Multiple circRNA mini-gene reporters were generated to evaluate the regulatory role of ECRRs. RT-PCR, qRT-PCR, northern blot, western blot, and flow cytometry assays were applied to assess the efficiency of artificial circRNA regulators on circRNA production in the presence or absence of RNase R treatment. Results: We engineered circRNA regulators by combining sequence-specific RNA binding motifs of human Pumilio 1 with functional domains that could form dimerization. We applied these engineered regulators to promote the circRNA production of the exogenous circRNA minigene reporter circGFP, thereby stimulating the functional GFP protein generation. Crucially, such regulation is in time-course dependent and dose-dependent manners with designed specificity. Moreover, the application of ECRRs could also stimulate circRNA biogenesis of another minigene reporter circScreen, suggesting that ECRRs can be commonly used to promote circRNA generation of exogenous reporters. Most importantly, ECRRs could be utilized to specifically promote the production of the endogenous circRNAs circ10720 and circBIRC6 as well. Conclusion: Our approach allows the creation of engineered regulators to target virtually any pre-mRNA in vivo, offering a novel avenue to investigate circRNA biogenesis and manipulate disease-related circRNA production.
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11
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Di Timoteo G, Dattilo D, Centrón-Broco A, Colantoni A, Guarnacci M, Rossi F, Incarnato D, Oliviero S, Fatica A, Morlando M, Bozzoni I. Modulation of circRNA Metabolism by m 6A Modification. Cell Rep 2021; 31:107641. [PMID: 32402287 DOI: 10.1016/j.celrep.2020.107641] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/24/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is an RNA modification well-known for its contribution to different processes controlling RNA metabolism, including splicing, stability, and translation of mRNA. Conversely, the role of m6A on the biogenesis and function of circular RNAs (circRNAs) has yet to be addressed. circRNAs belong to a class of covalently closed transcripts produced via a back-splicing reaction whereby a downstream 5' splice donor site fuses to an upstream 3' splice acceptor site. Starting from circ-ZNF609 as a study case, we discover that specific m6As control its accumulation and that METTL3 and YTHDC1 are required to direct the back-splicing reaction. This feature is shared with other circRNAs because we find a significant direct correlation among METTL3 requirement, YTHDC1 binding, and the ability of m6A exons to undergo back-splicing. Finally, because circ-ZNF609 displays the ability to be translated, we show that m6A modifications, through recognition by YTHDF3 and eIF4G2, modulate its translation.
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Dario Dattilo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alvaro Centrón-Broco
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Marco Guarnacci
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Danny Incarnato
- Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, the Netherlands
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
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12
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Abstract
Endometrial cancer (EC) is one of the most common malignant tumors of the female reproductive tract. EC patients have high morbidity and mortality rates and remain an important cause of cancer-related morbidity and mortality worldwide. More and more studies have shown that a large number of non-coding RNAs (such as microRNAs and long non-coding RNAs) are associated with the occurrence of diseases. Circular RNAs (circRNAs) is an endogenous non-coding RNA. It has a unique covalent structure. Many studies in recent years have found circRNAs differential expression in a variety of tumor tissues compared to matched normal tissues. In endometrial carcinoma, there also are multiple circRNAs differentially expressed and therefore circRNAs perhaps can be used as a diagnostic and prognosis biomarkers of EC. In this review, we described the biogenesis, function and characteristics of circRNAs, and the circRNAs with potential influence and clinical significance on the development of EC were summarized. Adenocarcinoma is the most common form of EC, so this review focuses on endometrioid adenocarcinoma.
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Affiliation(s)
- Jialu Guo
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310008, People's Republic of China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang Province, 310008, People's Republic of China
| | - Jinyi Tong
- Department of the Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310008, People's Republic of China.,Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang Province, 310008, People's Republic of China
| | - Jianfeng Zheng
- Department of Obstetrics and Gynecology, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, Zhejiang Province, 310008, People's Republic of China.,Department of Obstetrics and Gynecology, Affiliated Hangzhou Hospital, Nanjing Medical University, Hangzhou, Zhejiang Province, 310008, People's Republic of China
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13
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Zhang W, Qin P, Gong X, Huang L, Wang C, Chen G, Chen J, Wang L, Lv Z. Identification of circRNAs in the Liver of Whitespotted Bamboo Shark ( Chiloscyllium plagiosum). Front Genet 2020; 11:596308. [PMID: 33362857 PMCID: PMC7759564 DOI: 10.3389/fgene.2020.596308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022] Open
Abstract
Whitespotted bamboo shark (Chiloscyllium plagiosum), a member of the cartilaginous fish family, has an extremely large liver and demonstrates a strong regeneration ability and immune regulation. Circular RNAs (circRNAs) is an important class of non-coding RNAs. Increasing evidences suggest that circRNAs are a kind of potential regulators. Recently, researchers have isolated and identified different circRNAs from various species, while few reports were on the circRNAs of C. plagiosum. In this study, we have identified a total of 4,558 circRNAs in the liver of C. plagiosum. This finding suggests that circRNAs are not evenly distributed in the chromosomes and follow the GT-AG rule during cyclization. Alternative back-splicing might exist in shark circRNAs as shown by the authenticity identification of predicted circRNAs. The binding strength of circRNAs (<2,000 bp) and the detected miRNAs in shark liver were simultaneously analyzed to construct an mRNA–miRNA–circRNA network for the Glutathione S-transferase P1 gene, and the circRNA authenticity was simultaneously verified. Our data provide not only novel insights into the rich existence of circRNAs in marine animals, but also a basis for characterizing functions of identified circRNAs in the liver homeostasis of C. plagiosum.
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Affiliation(s)
- Wenjie Zhang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Ping Qin
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xiaoxia Gong
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lei Huang
- Hangzhou Hongqiao Sino-Science Gene Technology Co., Ltd., Hangzhou, China
| | - Chan Wang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Guiqian Chen
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jianqing Chen
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lei Wang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zhengbing Lv
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, China
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14
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Zucko D, Boris-Lawrie K. Circular RNAs Are Regulators of Diverse Animal Transcriptomes: One Health Perspective. Front Genet 2020; 11:999. [PMID: 33193584 PMCID: PMC7531264 DOI: 10.3389/fgene.2020.00999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
Derived from linear (parental) precursor mRNA, circRNA are recycled exons and introns whose ends are ligated. By titrating microRNAs and RNA binding proteins, circRNA interconnect networks of competing endogenous RNAs. Without altering chromosomal DNA, circRNA regulates skeletal muscle development and proliferation, lactation, ovulation, brain development, and responses to infections and metabolic stress. This review integrates emerging knowledge of circRNA activity coming from genome-wide characterizations in many clades of animals. circRNA research addresses one of the main pillars of the One Health vision – to improve the health and productivity of food animals and generate translational knowledge in animal species.
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Affiliation(s)
- Dora Zucko
- Department of Veterinary and Biomedical Sciences, Veterinary Medicine Graduate Program, University of Minnesota Twin Cities, Saint Paul, MN, United States
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, Veterinary Medicine Graduate Program, University of Minnesota Twin Cities, Saint Paul, MN, United States
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15
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. Wiley Interdiscip Rev RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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16
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Nahand JS, Jamshidi S, Hamblin MR, Mahjoubin-Tehran M, Vosough M, Jamali M, Khatami A, Moghoofei M, Baghi HB, Mirzaei H. Circular RNAs: New Epigenetic Signatures in Viral Infections. Front Microbiol 2020; 11:1853. [PMID: 32849445 PMCID: PMC7412987 DOI: 10.3389/fmicb.2020.01853] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Covalent closed circular RNAs (circRNAs) can act as a bridge between non-coding RNAs and coding messenger RNAs. CircRNAs are generated by a back-splicing mechanism during post-transcriptional processing and are abundantly expressed in eukaryotic cells. CircRNAs can act via the modulation of RNA transcription and protein production, and by the sponging of microRNAs (miRNAs). CircRNAs are now thought to be involved in many different biological and pathological processes. Some studies have suggested that the expression of host circRNAs is dysregulated in several types of virus-infected cells, compared to control cells. It is highly likely that viruses can use these molecules for their own purposes. In addition, some viral genes are able to produce viral circRNAs (VcircRNA) by a back-splicing mechanism. However, the viral genes that encode VcircRNAs, and their functions, are poorly studied. In this review, we highlight some new findings about the interaction of host circRNAs and viral infection. Moreover, the potential of VcircRNAs derived from the virus itself, to act as biomarkers and therapeutic targets is summarized.
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Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Sogol Jamshidi
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States.,Department of Dermatology, Harvard Medical School, Boston, MA, United States.,Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marzieh Jamali
- Department of Gynecology and Obstetrics, Mahdieh Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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17
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Goel A, Ward DG, Gordon NS, Abbotts B, Zeegers MP, Cheng KK, James ND, Bryan RT, Arnold R. Back-Splicing Transcript Isoforms (Circular RNAs) Affect Biologically Relevant Pathways and Offer an Additional Layer of Information to Stratify NMIBC Patients. Front Oncol 2020; 10:812. [PMID: 32670866 PMCID: PMC7326039 DOI: 10.3389/fonc.2020.00812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Circularized transcript isoforms due to back-splicing are increasingly being reported in different tissues types and pathological states including cancer. Since these circular RNAs (circRNAs) are more stable than linear messenger RNA their identification and profiling in tumor tissue could aid in stratifying patients and may serve as biomarkers. In this study, we have investigated the relationship between circRNA expression and tumor grade in a cohort of 58, mostly non-muscle-invasive bladder cancer patients. From 4571 circRNAs detected, we identified 157 that were significantly differentially expressed between tumor grades relative to the linear transcript. We demonstrated that such grade-related differences can be identified in an independent cohort, and that a large fraction of circRNAs can be, in principle, detected in urine. The differentially expressed circRNAs cluster into subgroups according to their co-expression, subgroups which are enriched for DNA repair, cell cycle and intracellular signaling genes. Since one proposed function of circRNAs is to interfere with gene-regulation by acting as microRNA “sponges,” candidates which were differentially expressed between tumor grades were investigated for potential miRNA target sites. By investigating the circRNAs from bladder cancer related pathways we demonstrated that the expression of these pathways, the circRNAs, and their parental genes are often decoupled and do not correlate, yet that some circRNAs do not follow this tendency. The present study provides the next step for the comprehensive evaluation of this novel class of RNAs in the context of non-muscle-invasive bladder cancer. Intriguingly, despite their possible function as microRNA sponges, they potentially affect host mRNA levels at the transcriptional stage, as compared to post-transcriptional control by miRNAs. Our analysis indicates differences of their activity between bladder cancer tumor stages, and their relative expression levels may provide an additional layer of information for patient stratification.
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Affiliation(s)
- Anshita Goel
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Naheema S Gordon
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ben Abbotts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Maurice P Zeegers
- NUTRIM School for Nutrition and Translational Research in Metabolism & CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, Netherlands
| | - K K Cheng
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicholas D James
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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18
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Czubak K, Sedehizadeh S, Kozlowski P, Wojciechowska M. An Overview of Circular RNAs and Their Implications in Myotonic Dystrophy. Int J Mol Sci 2019; 20:E4385. [PMID: 31500099 DOI: 10.3390/ijms20184385] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded covalently closed RNA rings. Biogenesis of circRNAs, which may occur co-transcriptionally and post-transcriptionally via a back-splicing mechanism, requires the presence of complementary and/or inverted repeat sequences in introns flanking back-spliced exons and is facilitated by RNA-binding proteins. CircRNAs are abundant across eukaryotes; however, their biological functions remain largely speculative. Recently, they have been emerging as new members of a gene regulatory network and contributing factors in various human diseases including cancer, neurological, muscular and cardiovascular disorders. In this review, we present an overview of the current knowledge about circRNAs biogenesis and their aberrant expression in various human disorders. In particular, we focus on the latest discovery of circRNAs global upregulation in myotonic dystrophy type 1 (DM1) skeletal muscles and the role these prospective biomarkers might have for prognosis and therapeutic response in DM1.
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19
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Hieronymus R, Müller S. Engineering of hairpin ribozyme variants for RNA recombination and splicing. Ann N Y Acad Sci 2019; 1447:135-143. [PMID: 30941784 DOI: 10.1111/nyas.14052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 11/28/2022]
Abstract
The hairpin ribozyme is a small, naturally occurring RNA that catalyzes the reversible cleavage of RNA substrates. Among the small endonucleolytic ribozymes, the hairpin ribozyme possesses the unique feature of the internal equilibrium between cleavage and ligation being shifted toward ligation. This allows control of the reaction outcome by structural design: fragments that are strongly bound to the ribozyme are preferentially ligated, whereas substrates that easily dissociate upon cleavage, such that they are not available for religation, are preferentially cleaved. We have made use of this characteristic feature in engineering a number of hairpin ribozyme variants by programmed conformational design that carry out cascades of cleavage and ligation reactions, and as a result mediate more complex RNA processing reactions. Here, we review our work on the engineering of hairpin ribozyme variants for RNA recombination and regular and back-splicing, and discuss the relevance of such activities in early life.
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Affiliation(s)
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Greifswald, Germany
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20
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Shen B, Wang Z, Li Z, Song H, Ding X. Circular RNAs: an emerging landscape in tumor metastasis. Am J Cancer Res 2019; 9:630-643. [PMID: 31105992 PMCID: PMC6511637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 06/09/2023] Open
Abstract
Circular RNAs (CircRNAs), the endogenous long noncoding RNAs, unlike linear RNAs, are structurally continuous, covalently closed loops without 5' cap or 3' polyadenylated tail. High-throughput RNA sequencing has enabled the discovery of several endogenous circRNAs in different species and tissues. The circRNAs mainly act as sponges to cytoplasmic microRNA, aid in protein translation, or interact with RNA-binding proteins to generate RNA-protein complexes which control transcription. Recently, circRNAs have been reported to participate in cancer pathogenesis, particularly tumor metastasis in humans, mainly due to their frequent aberrant expression in cancers. However, the detail molecular mechanism of circRNAs activity in tumor metastasis is still elusive. Some specifically expressed circRNAs can potentially be used as biomarkers and therapeutic targets for tumor treatment. Further understanding of the network interactions and regulation of circRNAs is paving the way for the identification of better therapeutic strategies in tumor metastasis. In this mini review, we have summarized the current state of research on functions and mechanisms of novel circRNAs that regulate tumorigenesis and have evaluated the relationship between dysregulation of circRNAs and tumor metastasis.
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Affiliation(s)
- Baile Shen
- The Medical School of Ningbo UniversityNingbo, Zhejiang, China
- The Gastroenterology Department of Ningbo First HospitalNingbo, Zhejiang, China
| | - Zheng Wang
- The Medical School of Zhejiang UniversityHangzhou, Zhejiang, China
- The Gastroenterology Department of Ningbo First HospitalNingbo, Zhejiang, China
| | - Zhuoya Li
- The Medical School of Ningbo UniversityNingbo, Zhejiang, China
- The Gastroenterology Department of Ningbo First HospitalNingbo, Zhejiang, China
| | - Haojun Song
- The Gastroenterology Department of Ningbo First HospitalNingbo, Zhejiang, China
| | - Xiaoyun Ding
- The Gastroenterology Department of Ningbo First HospitalNingbo, Zhejiang, China
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21
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Zhang J, Zhang X, Li C, Yue L, Ding N, Riordan T, Yang L, Li Y, Jen C, Lin S, Zhou D, Chen F. Circular RNA profiling provides insights into their subcellular distribution and molecular characteristics in HepG2 cells. RNA Biol 2019; 16:220-232. [PMID: 30614753 DOI: 10.1080/15476286.2019.1565284] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Circular RNA (circRNA) is a novel RNA molecule that has become a research focus recently. Although some research indicated that the circRNAs in different subcellular compartments could execute different regulatory functions, a panoramic analysis of the subcellular distribution and the transport mechanism of circRNA is still required. In this study, we comprehensively analyzed the subcellular distribution/characteristics and the transport mechanism, through systemically investigating the circRNA profiles among the subcellular fractions of HepG2 cell (nucleus, cytoplasm, mitochondria, ribosome, cytosol and exosome). CircRNAs were widely distributed among the subcellular fractions except in the mitochondria, with differences in the subcellular distribution/characteristics in terms of classification, length, GC content, alternative circularization and parental gene function. Further analysis indicated this might be due to the selective transportation mediated by the transport-related RNA binding proteins (RBPs). The circRNAs may follow the same transportation mechanism of linear RNAs, in which the RBPs specially recognize/transport the RNAs with the corresponding binding motifs. Interestingly, we found that the exosome could selectively package the circRNAs containing the purine-rich 5'-GMWGVWGRAG-3' motif, with the characteristic of 'garbage dumping' and 'intercellular signaling' functions. Besides, although we observed numerous circRNAs enriched in the ribosome, we did not reliably identify any unique-peptides from circRNAs using 3D-LC-MS/MS strategy. This suggests that circRNAs rarely function as translation templates in vivo like lincRNA. Our findings not only indicates the differential distributions/characteristics among the subcellular fractions, but also reveals the possible transportation mechanism. This provides an improved understanding of the life history and molecular behavior of circRNA in cells.
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Affiliation(s)
- Ju Zhang
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China
| | - Xiuli Zhang
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
| | - Cuidan Li
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
| | - Liya Yue
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China
| | - Nan Ding
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China
| | - Tim Riordan
- c Research and Development Department , NanoString Technologies, lnc , Seattle , WA , USA
| | - Li Yang
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
| | - Yang Li
- d Inspection Center , Beijing Protein Innovation Co., Ltd , Beijing , P.R. China
| | - Charles Jen
- e Marketing Department , Cold Spring (Beijing) Trading Co., Ltd , Beijing , P.R. China
| | - Sen Lin
- e Marketing Department , Cold Spring (Beijing) Trading Co., Ltd , Beijing , P.R. China
| | - Dongsheng Zhou
- f State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Microbiology and Epidemiology , Beijing , China
| | - Fei Chen
- a CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics , Chinese Academy of Sciences , Beijing , China.,b University of Chinese Academy of Sciences , Beijing , China
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22
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Abstract
Lung cancer is one of the most common cancers and the leading cause of cancer-related death worldwide. Despite encouraging results achieved with targeted therapy in recent years, the early diagnosis and treatment of lung cancer remains a major problem. Circular RNA (circRNA), a type of RNA with covalently closed continuous loop structures, has structural stability and certain tissue specificity. Recent studies have found that circRNAs have an important role in tumor development and are expected to be revealed as new targets for tumor prediction and treatment. Research on the biological functions and regulation mechanisms of circRNAs in lung cancer is in its infancy but is gathering momentum. In this review, we discuss the properties, biogenesis, biological function, and research progress of circRNAs in lung cancer to provide a theoretical foundation and new directions for studies on circRNAs in lung cancer.
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Affiliation(s)
- Yi Ma
- a Department of thoracic surgery , First Affiliated Hospital of China Medical University , Shenyang , Liaoning , China
| | - Xin Zhang
- a Department of thoracic surgery , First Affiliated Hospital of China Medical University , Shenyang , Liaoning , China
| | - Yi-Zhi Wang
- a Department of thoracic surgery , First Affiliated Hospital of China Medical University , Shenyang , Liaoning , China
| | - Hao Tian
- a Department of thoracic surgery , First Affiliated Hospital of China Medical University , Shenyang , Liaoning , China
| | - Shun Xu
- a Department of thoracic surgery , First Affiliated Hospital of China Medical University , Shenyang , Liaoning , China
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23
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Abstract
Covalently closed circular RNAs (circRNAs) are produced by precursor mRNA back-splicing of exons of thousands of genes in eukaryotes. circRNAs are generally expressed at low levels and often exhibit cell-type-specific and tissue-specific patterns. Recent studies have shown that their biogenesis requires spliceosomal machinery and can be modulated by both cis complementary sequences and protein factors. The functions of most circRNAs remain largely unexplored, but known functions include sequestration of microRNAs or proteins, modulation of transcription and interference with splicing, and even translation to produce polypeptides. However, challenges exist at multiple levels to understanding of the regulation of circRNAs because of their circular conformation and sequence overlap with linear mRNA counterparts. In this review, we survey the recent progress on circRNA biogenesis and function and discuss technical obstacles in circRNA studies.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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24
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Haque S, Harries LW. Circular RNAs (circRNAs) in Health and Disease. Genes (Basel) 2017; 8:genes8120353. [PMID: 29182528 PMCID: PMC5748671 DOI: 10.3390/genes8120353] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/22/2017] [Accepted: 11/22/2017] [Indexed: 01/17/2023] Open
Abstract
Splicing events do not always produce a linear transcript. Circular RNAs (circRNAs) are a class of RNA that are emerging as key new members of the gene regulatory milieu, which are produced by back-splicing events within genes. In circRNA formation, rather than being spliced in a linear fashion, exons can be circularised by use of the 3′ acceptor splice site of an upstream exon, leading to the formation of a circular RNA species. circRNAs have been demonstrated across species and have the potential to present genetic information in new orientations distinct from their parent transcript. The importance of these RNA players in gene regulation and normal cellular homeostasis is now beginning to be recognised. They have several potential modes of action, from serving as sponges for micro RNAs and RNA binding proteins, to acting as transcriptional regulators. In accordance with an important role in the normal biology of the cell, perturbations of circRNA expression are now being reported in association with disease. Furthermore, the inherent stability of circRNAs conferred by their circular structure and exonuclease resistance, and their expression in blood and other peripheral tissues in association with endosomes and microvesicles, renders them excellent candidates as disease biomarkers. In this review, we explore the state of knowledge on this exciting class of transcripts in regulating gene expression and discuss their emerging role in health and disease.
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Affiliation(s)
- Shahnaz Haque
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK.
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK.
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25
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Xie L, Mao M, Xiong K, Jiang B. Circular RNAs: A Novel Player in Development and Disease of the Central Nervous System. Front Cell Neurosci 2017; 11:354. [PMID: 29167634 PMCID: PMC5682331 DOI: 10.3389/fncel.2017.00354] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023] Open
Abstract
Circular RNAs (circRNAs) own unique capabilities to communicate with nucleic acids and ribonucleoproteins and are emerging as indispensable compositions of the regulatory messages encoded in the genome. Due to lack of 3′ termini, circRNAs are more resistant to degradation by exonuclease RNase R and possess greater stability than linear RNAs. Moreover, circRNAs can act as microRNA (miRNA) sponge and affect messenger RNA (mRNA) splicing and transcription. By virtue of their great stability and elaborate regulatory mechanisms of gene expression, circRNAs play important roles in certain physiological activities. The development, homeostasis and stress response of the central nervous system (CNS) depend upon precise temporal and spatial regulation of gene networks. Moreover, emerging evidence has revealed that circRNAs are spatiotemporally regulated and dynamically expressed during brain development; therefore, they can exert significant influences on CNS development and diseases. In this review, we highlight the biogenesis of circRNAs and their central roles in regulation of CNS development and diseases.
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Affiliation(s)
- Lili Xie
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Mao Mao
- Departments of Ophthalmology and Anatomy, Institute for Human Genetics, UCSF School of Medicine, San Francisco, CA, United States
| | - Kun Xiong
- Department of Human Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Bing Jiang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
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26
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Rong D, Sun H, Li Z, Liu S, Dong C, Fu K, Tang W, Cao H. An emerging function of circRNA-miRNAs-mRNA axis in human diseases. Oncotarget 2017; 8:73271-73281. [PMID: 29069868 PMCID: PMC5641211 DOI: 10.18632/oncotarget.19154] [Citation(s) in RCA: 368] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/01/2017] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs), a novel class of long noncoding RNAs, are characterized by a covalently closed continuous loop without 5′ or 3′ polarities structure and have been widely found in thousands of lives including plants, animals and human beings. Utilizing the high-throughput RNA sequencing (RNA-seq) technology, recent findings have indicated thata great deal of circRNAs, which are endogenous, stable, widely expressed in mammalian cells, often exhibit cell type-specific, tissue-specific or developmental-stage-specific expression. Evidences are arising that some circRNAs might regulate microRNA (miRNA) function as microRNA sponges and play a significant role in transcriptional control. circRNAs associate with related miRNAs and the circRNA-miRNA axes are involved in a serious of disease pathways such as apoptosis, vascularization, invasion and metastasis. In this review, we generalize and analyse the aspects including synthesis, characteristics, classification, and several regulatory functions of circRNAs and highlight the association between circRNAs dysregulation by circRNA-miRNA-mRNA axis and sorts of diseases including cancer- related and non-cancer diseases.”
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Affiliation(s)
- Dawei Rong
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Handong Sun
- Department of Oncology Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhouxiao Li
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shuheng Liu
- Department of Neurosurgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chaoxi Dong
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kai Fu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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27
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Abstract
Circular RNAs (circ-RNAs), a novel class of noncoding RNAs, are a popular topic in animal research because they have potential as post-transcriptional regulators and diagnostic markers. Research in plants is only now emerging, but indicates that circ-RNAs could also be a crucial class of noncoding regulators.
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Affiliation(s)
- Sang-Moo Lee
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea; Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34141, South Korea
| | - Hyun Gi Kong
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea; Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34141, South Korea.
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28
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Abstract
Circular RNAs (CircRNAs) were first identified as a viroid and later found to also be an endogenous RNA splicing product in eukaryotes. In recent years, a series of RNA-sequencing analyses from a diverse range of eukaryotes have shed new light on these eukaryotic circRNAs, revealing dynamic expression patterns in various developmental stages and physiological conditions. In this review, we focus on circRNAs implicated in stress response pathways and explore potential mechanisms underlying their regulation. To date, circRNAs have been shown to act as scaffolds in the assembly of protein complexes, sequester proteins from native subcellular localization, activate transcription of parental genes, inhibit RNA-protein interactions, and function as regulators of microRNA activity. Although the mechanism modulating circRNA levels during stress remains unclear, circRNAs are shown to be regulated during biogenesis, degradation, and exportation. As circRNAs do not have 5' and 3' ends, there are no entry points for exoribonucleases to initiate degradation. Such inherent stability makes this class of RNA a strong candidate to maintain homeostasis in the face of environmental challenges.
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Affiliation(s)
- Joseph W Fischer
- a McKusick-Nathans Institute of Genetic Medicine, School of Medicine , Johns Hopkins University , Baltimore , MD , USA.,b Department of Biochemistry and Molecular Biology , Bloomberg School of Public Health, Johns Hopkins University , Baltimore , MD , USA
| | - Anthony K L Leung
- a McKusick-Nathans Institute of Genetic Medicine, School of Medicine , Johns Hopkins University , Baltimore , MD , USA.,b Department of Biochemistry and Molecular Biology , Bloomberg School of Public Health, Johns Hopkins University , Baltimore , MD , USA.,c Department of Oncology , School of Medicine, Johns Hopkins University , Baltimore , MD , USA
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29
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Abstract
Circular RNAs (circRNAs) are broadly identified from precursor mRNA (pre-mRNA) back-splicing across various species. Recent studies have suggested a cell-/tissue- specific manner of circRNA expression. However, the distinct expression pattern of circRNAs among species and its underlying mechanism still remain to be explored. Here, we systematically compared circRNA expression from human and mouse, and found that only a small portion of human circRNAs could be determined in parallel mouse samples. The conserved circRNA expression between human and mouse is correlated with the existence of orientation-opposite complementary sequences in introns that flank back-spliced exons in both species, but not the circRNA sequences themselves. Quantification of RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns by Complementary Sequence Index (CSI) identifies that among all types of complementary sequences, SINEs, especially Alu elements in human, contribute the most for circRNA formation and that their diverse distribution across species leads to the increased complexity of circRNA expression during species evolution. Together, our integrated and comparative reference catalog of circRNAs in different species reveals a species-specific pattern of circRNA expression and suggests a previously under-appreciated impact of fast-evolved SINEs on the regulation of (circRNA) gene expression.
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Affiliation(s)
- Rui Dong
- a Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai , China.,c University of Chinese Academy of Sciences , Beijing , China
| | - Xu-Kai Ma
- a Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai , China.,c University of Chinese Academy of Sciences , Beijing , China
| | - Ling-Ling Chen
- b State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , Chinese Academy of Sciences , Shanghai , China.,c University of Chinese Academy of Sciences , Beijing , China.,d School of Life Science and Technology, ShanghaiTech University , Shanghai , China
| | - Li Yang
- a Key Laboratory of Computational Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences , Shanghai , China.,c University of Chinese Academy of Sciences , Beijing , China.,d School of Life Science and Technology, ShanghaiTech University , Shanghai , China
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30
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Abstract
Unlike linear RNAs terminated with 5' caps and 3' tails, circular RNAs are characterized by covalently closed loop structures with neither 5' to 3' polarity nor polyadenylated tail. This intrinsic characteristic has led to the general under-estimation of the existence of circular RNAs in previous polyadenylated transcriptome analyses. With the advent of specific biochemical and computational approaches, a large number of circular RNAs from back-spliced exons (circRNAs) have been identified in various cell lines and across different species. Recent studies have uncovered that back-splicing requires canonical spliceosomal machinery and can be facilitated by both complementary sequences and specific protein factors. In this review, we highlight our current understanding of the regulation of circRNA biogenesis, including both the competition between splicing and back-splicing and the previously under-appreciated alternative circularization.
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Affiliation(s)
- Ling-Ling Chen
- a State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences ; Shanghai , China
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31
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Boeckel JN, Jaé N, Heumüller AW, Chen W, Boon RA, Stellos K, Zeiher AM, John D, Uchida S, Dimmeler S. Identification and Characterization of Hypoxia-Regulated Endothelial Circular RNA. Circ Res 2015; 117:884-90. [PMID: 26377962 DOI: 10.1161/circresaha.115.306319] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/16/2015] [Indexed: 02/06/2023]
Abstract
RATIONALE Circular RNAs (circRNAs) are noncoding RNAs generated by back splicing. Back splicing has been considered a rare event, but recent studies suggest that circRNAs are widely expressed. However, the expression, regulation, and function of circRNAs in vascular cells is still unknown. OBJECTIVE Here, we characterize the expression, regulation, and function of circRNAs in endothelial cells. METHODS AND RESULTS Endothelial circRNAs were identified by computational analysis of ribo-minus RNA generated from human umbilical venous endothelial cells cultured under normoxic or hypoxic conditions. Selected circRNAs were biochemically characterized, and we found that the majority of them lacks polyadenylation, is resistant to RNase R digestion and localized to the cytoplasm. We further validated the hypoxia-induced circRNAs cZNF292, cAFF1, and cDENND4C, as well as the downregulated cTHSD1 by reverse transcription polymerase chain reaction in cultured endothelial cells. Cloning of cZNF292 validated the predicted back splicing of exon 4 to a new alternative exon 1A. Silencing of cZNF292 inhibited cZNF292 expression and reduced tube formation and spheroid sprouting of endothelial cells in vitro. The expression of pre-mRNA or mRNA of the host gene was not affected by silencing of cZNF292. No validated microRNA-binding sites for cZNF292 were detected in Argonaute high-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation data sets, suggesting that cZNF292 does not act as a microRNA sponge. CONCLUSIONS We show that the majority of the selected endothelial circRNAs fulfill all criteria of bona fide circRNAs. The circRNA cZNF292 exhibits proangiogenic activities in vitro. These data suggest that endothelial circRNAs are regulated by hypoxia and have biological functions.
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Affiliation(s)
- Jes-Niels Boeckel
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Nicolas Jaé
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Andreas W Heumüller
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Wei Chen
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Reinier A Boon
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Konstantinos Stellos
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Andreas M Zeiher
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - David John
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Shizuka Uchida
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.)
| | - Stefanie Dimmeler
- From the Institute for Cardiovascular Regeneration, Center for Molecular Medicine, University Frankfurt, Frankfurt, Germany (J.-N.B., N.J., A.W.H., R.A.B., K.S., D.J., S.U., S.D.); Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, Germany (W.C.); Department of Cardiology, Internal Medicine III, Goethe-University Hospital, Frankfurt, Germany (K.S., A.M.Z.); and German Center for Cardiovascular Research (DZHK) (J.-N.B., N.J., W.C., R.A.B., K.S., D.J., A.M.Z., S.U., S.D.).
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