1
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Digby B, Finn S, Ó Broin P. Computational approaches and challenges in the analysis of circRNA data. BMC Genomics 2024; 25:527. [PMID: 38807085 PMCID: PMC11134749 DOI: 10.1186/s12864-024-10420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Circular RNAs (circRNA) are a class of non-coding RNA, forming a single-stranded covalently closed loop structure generated via back-splicing. Advancements in sequencing methods and technologies in conjunction with algorithmic developments of bioinformatics tools have enabled researchers to characterise the origin and function of circRNAs, with practical applications as a biomarker of diseases becoming increasingly relevant. Computational methods developed for circRNA analysis are predicated on detecting the chimeric back-splice junction of circRNAs whilst mitigating false-positive sequencing artefacts. In this review, we discuss in detail the computational strategies developed for circRNA identification, highlighting a selection of tool strengths, weaknesses and assumptions. In addition to circRNA identification tools, we describe methods for characterising the role of circRNAs within the competing endogenous RNA (ceRNA) network, their interactions with RNA-binding proteins, and publicly available databases for rich circRNA annotation.
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Affiliation(s)
- Barry Digby
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland.
| | - Stephen Finn
- Discipline of Histopathology, School of Medicine, Trinity College Dublin and Cancer Molecular Diagnostic Laboratory, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
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2
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Lin HH, Chang CY, Huang YR, Shen CH, Wu YC, Chang KL, Lee YC, Lin YC, Ting WC, Chien HJ, Zheng YF, Lai CC, Hsiao KY. Exon Junction Complex Mediates the Cap-Independent Translation of Circular RNA. Mol Cancer Res 2023; 21:1220-1233. [PMID: 37527157 DOI: 10.1158/1541-7786.mcr-22-0877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/22/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Evidence that circular RNAs (circRNA) serve as protein template is accumulating. However, how the cap-independent translation is controlled remains largely uncharacterized. Here, we show that the presence of intron and thus splicing promote cap-independent translation. By acquiring the exon junction complex (EJC) after splicing, the interaction between circRNA and ribosomes was promoted, thereby facilitating translation. Prevention of splicing by treatment with spliceosome inhibitor or mutating splicing signal hindered cap-independent translation of circRNA. Moreover, EJC-tethering using Cas13 technology reconstituted EJC-dependent circRNA translation. Finally, the level of a coding circRNA from succinate dehydrogenase assembly factor 2 (circSDHAF2) was found to be elevated in the tumorous tissues from patients with colorectal cancer, and shown to be critical in tumorigenesis of colorectal cancer in both cell and murine models. These findings reveal that EJC-dependent control of circSDHAF2 translation is involved in the regulation of oncogenic pathways. IMPLICATIONS EJC-mediated cap-independent translation of circRNA is implicated in the tumorigenesis of colorectal cancer.
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Affiliation(s)
- Hui-Hsuan Lin
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chiu-Yuan Chang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ren Huang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Che-Hung Shen
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Yu-Chen Wu
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kai-Li Chang
- Department of Physiology, National Cheng Kung University, Tainan, Taiwan
| | - Yueh-Chun Lee
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ya-Chi Lin
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Wen-Chien Ting
- Division of Colorectal Surgery, Department of Surgery, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Han-Ju Chien
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Yi-Feng Zheng
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kuei-Yang Hsiao
- Doctoral Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, Taiwan
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Doctoral Program in Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung
- Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung
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3
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Pisignano G, Michael DC, Visal TH, Pirlog R, Ladomery M, Calin GA. Going circular: history, present, and future of circRNAs in cancer. Oncogene 2023; 42:2783-2800. [PMID: 37587333 PMCID: PMC10504067 DOI: 10.1038/s41388-023-02780-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023]
Abstract
To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.
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Affiliation(s)
- Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - David C Michael
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tanvi H Visal
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radu Pirlog
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol, BS16 1QY, UK
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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4
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Bagheri Moghaddam M, Maleki M, Oveisee M, Bagheri Moghaddam M, Arabian M, Malakootian M. Circular RNAs: New Players in Cardiomyopathy. Genes (Basel) 2022; 13:genes13091537. [PMID: 36140705 PMCID: PMC9498503 DOI: 10.3390/genes13091537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Cardiomyopathies comprise a heterogeneous group of cardiac diseases identified by myocardium disorders and diminished cardiac function. They often lead to heart failure or heart transplantation and constitute one of the principal causes of morbidity and mortality worldwide. Circular RNAs (circRNAs) are a novel type of noncoding RNAs. They are covalently closed and single-stranded and derived from the exons and introns of genes by alternative splicing. This specific structure renders them resistant to exonuclease digestion. Many recent studies have demonstrated that circRNAs are highly abundant and conserved and can play central roles in biological functions such as microRNA (miRNA) sponging, splicing, and transcription regulation. Emerging evidence indicates that circRNAs can play significant roles in cardiovascular diseases, including cardiomyopathies. In this review, we briefly describe the current understanding regarding the classification, nomenclature, characteristics, and function of circRNAs and report recent significant findings concerning the roles of circRNAs in cardiomyopathies. Furthermore, we discuss the clinical application potential of circRNAs as the therapeutic targets and diagnostic biomarkers of cardiomyopathies.
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Affiliation(s)
- Maedeh Bagheri Moghaddam
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 141171311, Iran
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Maziar Oveisee
- School of Medicine, Bam University of Medical Sciences, Bam 7661771967, Iran
| | - Mahrokh Bagheri Moghaddam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Maedeh Arabian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
- Correspondence: ; Tel.: +98-2123923033; Fax: +98-2122663213
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Lee YC, Wang WY, Lin HH, Huang YR, Lin YC, Hsiao KY. The Functional Roles and Regulation of Circular RNAs during Cellular Stresses. Noncoding RNA 2022; 8:ncrna8030038. [PMID: 35736635 PMCID: PMC9228399 DOI: 10.3390/ncrna8030038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of regulatory RNA involved in many biological, physiological and pathological processes by functioning as a molecular sponge, transcriptional/epigenetic/splicing regulator, modulator of protein–protein interactions, and a template for encoding proteins. Cells are constantly dealing with stimuli from the microenvironment, and proper responses rely on both the precise control of gene expression networks and protein–protein interactions at the molecular level. The critical roles of circRNAs in the regulation of these processes have been heavily studied in the past decades. However, how the microenvironmental stimulation controls the circRNA biogenesis, cellular shuttling, translation efficiency and degradation globally and/or individually remains largely uncharacterized. In this review, how the impact of major microenvironmental stresses on the known transcription factors, splicing modulators and epitranscriptomic regulators, and thereby how they may contribute to the regulation of circRNAs, is discussed. These lines of evidence will provide new insight into how the biogenesis and functions of circRNA can be precisely controlled and targeted for treating human diseases.
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Affiliation(s)
- Yueh-Chun Lee
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan;
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Wei-Yu Wang
- Division of Hemato-Oncology, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi City 60002, Taiwan;
| | - Hui-Hsuan Lin
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Yi-Ren Huang
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Ya-Chi Lin
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Kuei-Yang Hsiao
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
- Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan;
- Ph.D. Program in Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
- Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
- Bachelor Program of Biotechnology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan
- Correspondence: ; Tel.: +886-42-284-0468 (ext. 8433)
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6
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Ottolia M, John S, Hazan A, Goldhaber JI. The Cardiac Na + -Ca 2+ Exchanger: From Structure to Function. Compr Physiol 2021; 12:2681-2717. [PMID: 34964124 DOI: 10.1002/cphy.c200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ca2+ homeostasis is essential for cell function and survival. As such, the cytosolic Ca2+ concentration is tightly controlled by a wide number of specialized Ca2+ handling proteins. One among them is the Na+ -Ca2+ exchanger (NCX), a ubiquitous plasma membrane transporter that exploits the electrochemical gradient of Na+ to drive Ca2+ out of the cell, against its concentration gradient. In this critical role, this secondary transporter guides vital physiological processes such as Ca2+ homeostasis, muscle contraction, bone formation, and memory to name a few. Herein, we review the progress made in recent years about the structure of the mammalian NCX and how it relates to function. Particular emphasis will be given to the mammalian cardiac isoform, NCX1.1, due to the extensive studies conducted on this protein. Given the degree of conservation among the eukaryotic exchangers, the information highlighted herein will provide a foundation for our understanding of this transporter family. We will discuss gene structure, alternative splicing, topology, regulatory mechanisms, and NCX's functional role on cardiac physiology. Throughout this article, we will attempt to highlight important milestones in the field and controversial topics where future studies are required. © 2021 American Physiological Society. Compr Physiol 12:1-37, 2021.
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Affiliation(s)
- Michela Ottolia
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Scott John
- Department of Medicine (Cardiology), UCLA, Los Angeles, California, USA
| | - Adina Hazan
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Joshua I Goldhaber
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
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7
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CircNCX1: the "Lord of the Ring" in the Heart - Insight into Its Sequence Characteristic, Expression, Molecular Mechanisms, and Clinical Application. J Cardiovasc Transl Res 2021; 15:571-586. [PMID: 34642871 DOI: 10.1007/s12265-021-10176-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs with regulatory activity and regarded as new types of therapeutic targets in diseases such as cancers. By means of RNA-Seq technology, numerous cardiac circRNAs were discovered. Although some candidates were detected to involve in heart disease in murine model, relative low sequence conservation and expression level of their human homologs might result in an insignificant, even distinct effect in the human heart. Therefore, the therapeutic significance of circRNAs should be more strictly considered. It is also necessary to discuss which circRNA is suitable for being applied in heart disease treatment. Here, we are willing to introduce a ~ 1830 nt circular transcript generated from single exon of sodium/calcium exchanger 1 (ncx1) gene (also called solute carrier family 8 member A1, slc8a1), usually named circNCX1 or circSLC8A1, which is gradually coming into our view. circNCX1 is one of the most cardiac-enriched circRNAs. It is widely existent in vertebrate and relatively conserved, indicating its indispensability during the evolution of species. Indeed, circNCX1 was shown to involve in heart development by some expression analysis. It was further revealed that the dysregulation of circNCX1 is one of the key pathogeneses of heart diseases including ischemic cardiac injury and hypertrophic cardiomyopathy. To make the significance of circNCX1 in the heart clear, we comprehensively dissected circNCX1 in the aspects of its parental gene structure, conservation, biogenesis and expression profiles, function, molecular mechanisms, and clinical application in this review. New medicine or therapeutic schedules based on circNCX1 are expected in the future.
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8
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Abstract
CircRNAs are a subclass of lncRNAs that have been found to be abundantly present in a wide range of species, including humans. CircRNAs are generally produced by a noncanonical splicing event called backsplicing that is dependent on the canonical splicing machinery, giving rise to circRNAs classified into three main categories: exonic circRNA, circular intronic RNA, and exon-intron circular RNA. Notably, circRNAs possess functional importance and display their functions through different mechanisms of action including sponging miRNAs, or even being translated into functional proteins. In addition, circRNAs also have great potential as biomarkers, particularly in cancer, thanks to their high stability, tissue type and developmental stage specificity, and their presence in biological fluids, which make them promising candidates as noninvasive biomarkers. In this chapter, we describe the most commonly used techniques for the study of circRNAs as cancer biomarkers, including high-throughput techniques such as RNA-Seq and microarrays, and other methods to analyze the presence of specific circRNAs in patient samples.
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Affiliation(s)
- Carla Solé
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Gartze Mentxaka
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain. .,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain. .,Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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9
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Decoding the complexity of circular RNAs in cardiovascular disease. Pharmacol Res 2021; 171:105766. [PMID: 34271160 DOI: 10.1016/j.phrs.2021.105766] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/23/2021] [Accepted: 07/09/2021] [Indexed: 12/23/2022]
Abstract
Circular RNAs (circRNAs) are a new class of covalently circularized noncoding RNAs widely expressed in the human heart. Emerging evidence suggests they have a regulatory role in a variety of cardiovascular diseases (CVDs). This review's current focus includes our understanding of circRNA classification, biogenesis, function, stability, degradation mechanisms, and their roles in various cardiovascular disease conditions. Our knowledge of circRNA, the relatively recent member of the noncoding RNA family, is still in its infancy; however, recent literature proposes circRNAs may be promising targets for the understanding and treatment of CVD.
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10
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Tang L, Li P, Jang M, Zhu W. Circular RNAs and Cardiovascular Regeneration. Front Cardiovasc Med 2021; 8:672600. [PMID: 33928139 PMCID: PMC8076501 DOI: 10.3389/fcvm.2021.672600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/22/2021] [Indexed: 01/22/2023] Open
Abstract
circular RNAs (circRNAs) are a type of non-coding RNAs that are widely present in eukaryotic cells. They have the characteristics of stable structure, high abundance, and cell or tissue specific expression. circRNAs are single-stranded RNAs that are covalently back spliced to form closed circular loops. They may participate in gene expression and regulation through a variety of action modes. circRNAs can encode proteins or function by acting as miRNA sponges for protein translation. Since 2016, a growing number of research studies have shown that circRNAs play important role in the pathogenesis of cardiovascular disease. With the construction of circRNA database, the differential expression of circRNAs in the heart tissue samples from different species and the gradual elucidation of its mode of action in disease may become an ideal diagnosis biomarker and an effective therapeutic target. What can be expected surely has a broader application prospect. In this review, we summarize recent publications on circRNA biogenesis, expression profiles, functions, and the most recent studies of circRNAs in the field of cardiovascular diseases with special emphasis on cardiac regeneration.
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Affiliation(s)
- Ling Tang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Pengsheng Li
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Michelle Jang
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
| | - Wuqiang Zhu
- Department of Cardiovascular Diseases, Physiology and Biomedical Engineering, Center of Regenerative Medicine, Mayo Clinic, Scottsdale, AZ, United States
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11
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Yang Z, He T, Chen Q. The Roles of CircRNAs in Regulating Muscle Development of Livestock Animals. Front Cell Dev Biol 2021; 9:619329. [PMID: 33748107 PMCID: PMC7973088 DOI: 10.3389/fcell.2021.619329] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/18/2021] [Indexed: 12/25/2022] Open
Abstract
The muscle growth and development of livestock animals is a complex, multistage process, which is regulated by many factors, especially the genes related to muscle development. In recent years, it has been reported frequently that circular RNAs (circRNAs) are involved widely in cell proliferation, cell differentiation, and body development (including muscle development). However, the research on circRNAs in muscle growth and development of livestock animals is still in its infancy. In this paper, we briefly introduce the discovery, classification, biogenesis, biological function, and degradation of circRNAs and focus on the molecular mechanism and mode of action of circRNAs as competitive endogenous RNAs in the muscle development of livestock and poultry. In addition, we also discuss the regulatory mechanism of circRNAs on muscle development in livestock in terms of transcription, translation, and mRNAs. The purpose of this article is to discuss the multiple regulatory roles of circRNAs in the process of muscle development in livestock, to provide new ideas for the development of a new co-expression regulation network, and to lay a foundation for enriching livestock breeding and improving livestock economic traits.
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Affiliation(s)
- Zhenguo Yang
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Tianle He
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qingyun Chen
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
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12
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Miao Q, Ni B, Tang J. Coding potential of circRNAs: new discoveries and challenges. PeerJ 2021; 9:e10718. [PMID: 33552732 PMCID: PMC7819118 DOI: 10.7717/peerj.10718] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
The circular (circ)RNAs are a newly recognized group of noncoding (nc)RNAs. Research to characterize the functional features of circRNAs has uncovered distinctive profiles of conservation, stability, specificity and complexity. However, a new line of evidence has indicated that although circRNAs can function as ncRNAs, such as in the role of miRNA sponges, they are also capable of coding proteins. This discovery is no accident. In the last century, scientist detected the ability of translate in some virus and artificial circRNAs. Artificial circRNA translation products are usually nonfunctional, whereas natural circRNA translation products are completely different. Those new proteins have various functions, which greatly broadens the new ideas and research direction for our research. These series findings also raise questions about whether circRNA is still classified as non-coding RNA. Here, we summarize the evidence concerning translation potential of circRNAs, including synthetic and endogenous circRNA translation ability, and discuss the mechanisms of circRNA translation.
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Affiliation(s)
- Qingqing Miao
- Dermatology Department of The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.,Department of Dermatology, the 901th Hospital of the Joint Logistics Support Force of PLA Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Bing Ni
- Department of Pathophysiology, Third Military Medical University, Chongqing, China
| | - Jun Tang
- Dermatology Department of The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.,Department of Dermatology, the 901th Hospital of the Joint Logistics Support Force of PLA Affiliated to Anhui Medical University, Hefei, Anhui, China
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13
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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14
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Yuan Y, Xu L, Geng Z, Liu J, Zhang L, Wu Y, He D, Qu P. The role of non-coding RNA network in atherosclerosis. Life Sci 2020; 265:118756. [PMID: 33189816 DOI: 10.1016/j.lfs.2020.118756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/10/2020] [Indexed: 12/26/2022]
Abstract
Atherosclerosis is the primary culprit of cardiovascular and cerebrovascular diseases. Also, atherogenesis and the development of atherosclerosis involve endothelial cells, monocytes/macrophages, smooth myocytes, and others. Increasingly, studies have found that non-coding RNA (ncRNA) which can regulate apoptosis, pyroptosis, autophagy, proliferation, and monocyte migration participates in atherogenesis and progress of atherosclerosis by the above. The ncRNA networks may be essential in regulating the complicated process of atherosclerosis. Accordingly, this review delves into the regulatory roles of ncRNA, which were introduced previously. The answer above is particularly crucial to explain further the regulatory mechanism of ncRNA in cardiovascular disorders. Furthermore, we discuss the possibility and related research of ncRNAs as a biomarker and therapeutic target for the prevention, diagnosis, and treatment of atherosclerosis.
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Affiliation(s)
- Yuchan Yuan
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116023, People's Republic of China
| | - Ling Xu
- Department of clinical laboratory, Xinhua Hospital Affiliated to Dalian University, Dalian 116021, People's Republic of China
| | - Zhaohong Geng
- Department of Cardiology, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, People's Republic of China
| | - Jingjing Liu
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116023, People's Republic of China
| | - Lijiao Zhang
- Department of Cardiology, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, People's Republic of China
| | - Yuhang Wu
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116023, People's Republic of China
| | - Dan He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China; Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing 100191, People's Republic of China.
| | - Peng Qu
- Institute of Heart and Vessel Diseases, The Second Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian 116023, People's Republic of China; Department of Cardiology, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, People's Republic of China.
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15
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Abstract
Circular RNAs (circRNAs) are covalently circularized RNA moieties that despite being relatively abundant were only recently identified and have only begun to be investigated within the last couple of years. Even though there are many thousands of genes that appear capable of producing circRNAs, and the fact that many circRNAs appear to be highly evolutionarily conserved, the function of all but a few remain to be fully explored. What has been determined, however, is that circRNAs play key regulatory roles in many aspects of biology with focus being given to their function in cancer. Most of the studies to date have found that circRNAs act as master regulator of gene expression most often than not acting to regulate levels though sequestration or "sponging" of other gene expression regulators, particularly miRNAs. They can also function directly modulating transcription, or by interfering with splicing mechanisms. Some circRNAs can also be translated into functional proteins or peptides. A combination of tissue and developmental stage specific expression along with an innate resistance to RNAse activity means that circRNAs show perhaps their greatest potential as novel biomarkers of cancer. In this chapter we consider the current state of knowledge regarding these molecules, their synthesis, function, and association with cancer. We also consider some of the challenges that remain to be overcome to allow this emerging class of RNAs to fulfill their potential in clinical practice.
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Affiliation(s)
- Carla Solé
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain
| | - Charles Henderson Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom.
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16
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Jahn C, Bär C, Thum T. CircSlc8a1, breaking a vicious circle in cardiac hypertrophy. Cardiovasc Res 2020; 115:1946-1947. [PMID: 31147691 DOI: 10.1093/cvr/cvz147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Christopher Jahn
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl Neuberg Str-1, Hannover, Germany
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl Neuberg Str-1, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Carl Neuberg Str-1, Hannover, Germany
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17
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Li B, Li Y, Hu L, Liu Y, Zhou Q, Wang M, An Y, Li P. Role of Circular RNAs in the Pathogenesis of Cardiovascular Disease. J Cardiovasc Transl Res 2020; 13:572-583. [PMID: 32399680 DOI: 10.1007/s12265-019-09912-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are single-strand covalently closed circular noncoding RNAs that are endogenous transcripts generated from linear precursor mRNA through a backsplicing mechanism. With the development of high-throughput sequencing technology, a number of circRNAs have been identified and proved to play key roles in various pathophysiological processes, such as metabolic diseases, cancers, and cardiovascular diseases. An increasing number of studies have shown that circRNAs are widely expressed in cardiac tissues and play important roles in the development of multiple cardiovascular diseases. Here, we review the current understanding of circRNA biogenesis and functions and the roles of circRNAs in cardiovascular diseases. We also highlight the molecular mechanisms underlying the role of circRNAs in the pathogenesis of cardiovascular diseases. A better understanding of the biological function of circRNAs in cardiovascular diseases will be helpful for the development of effective biomarkers for the diagnosis and treatment of these diseases.
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Affiliation(s)
- Baowei Li
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Yuzhen Li
- Department of Pathophysiology, Institute of Basic Medical Science, PLA General Hospital, Beijing, 100853, China
| | - Longgang Hu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, 266021, China
| | - Ying Liu
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Qihui Zhou
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Man Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Yi An
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, 266021, China.
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China.
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18
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Humphreys DT, Fossat N, Demuth M, Tam PPL, Ho JWK. Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing. Nucleic Acids Res 2020; 47:e123. [PMID: 31435647 PMCID: PMC6846653 DOI: 10.1093/nar/gkz718] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/23/2019] [Accepted: 08/08/2019] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNA) are a unique class of transcripts that can only be identified from sequence alignments spanning discordant junctions, commonly referred to as backsplice junctions (BSJ). Canonical splicing is also linked with circRNA biogenesis either from the parental transcript or internal to the circRNA, and is not fully utilized in circRNA software. Here we present Ularcirc, a software tool that integrates the visualization of both BSJ and forward splicing junctions and provides downstream analysis of selected circRNA candidates. Ularcirc utilizes the output of CIRI, circExplorer, or raw chimeric output of the STAR aligner and assembles BSJ count table to allow multi-sample analysis. We used Ularcirc to identify and characterize circRNA from public and in-house generated data sets and demonstrate how it can be used to (i) discover novel splicing patterns of parental transcripts, (ii) detect internal splicing patterns of circRNA, and (iii) reveal the complexity of BSJ formation. Furthermore, we identify circRNA that have potential open reading frames longer than their linear sequence. Finally, we detected and validated the presence of a novel class of circRNA generated from ApoA4 transcripts whose BSJ derive from multiple non-canonical splicing sites within coding exons. Ularcirc is accessed via https://github.com/VCCRI/Ularcirc.
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Affiliation(s)
- David T Humphreys
- Victor Chang Cardiac Research Institute.,University of New South Wales, Sydney, Australia
| | - Nicolas Fossat
- Embryology Unit, Children's Medical Research Institute.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | | | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute.,University of New South Wales, Sydney, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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19
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Xie R, Zhang Y, Zhang J, Li J, Zhou X. The Role of Circular RNAs in Immune-Related Diseases. Front Immunol 2020; 11:545. [PMID: 32300345 PMCID: PMC7142234 DOI: 10.3389/fimmu.2020.00545] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/10/2020] [Indexed: 02/05/2023] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs with a covalently closed loop structure without a 3′ polyadenylation [poly-(A)] tail or a 5′ cap. They used to be considered as the occasional and useless products of RNA splicing errors because they could not be detected by traditional RNA sequencing technology. Benefiting from the development of specific biochemical and computational approaches, researchers showed that circRNAs are universally expressed and functional. Further studies have revealed their important functions regarding regulating gene expression at the transcriptional and post-transcriptional levels. These functions include acting as microRNA (miRNA) sponges, binding to RNA-binding proteins (RBPs), acting as transcriptional regulatory factors, and serving as translation templates. The advances in circRNA research has opened researchers' eyes to a new area of research on the roles of circRNAs in the pathogenesis of various diseases, especially at the immune level because of the close relationship between circRNAs and the immune response. Emerging research indicates that circRNAs could act as potential biomarkers related to diagnosis, therapeutic effects, and prognosis, and they may be effective therapeutic targets in immunological disorders, including certain diseases that are currently difficult to treat.
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Affiliation(s)
- Rou Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yongxin Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jun Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China College of Stomatology, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Sichuan University, Chengdu, China
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
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20
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Guria A, Sharma P, Natesan S, Pandi G. Circular RNAs-The Road Less Traveled. Front Mol Biosci 2020; 6:146. [PMID: 31998746 PMCID: PMC6965350 DOI: 10.3389/fmolb.2019.00146] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs are the most recent addition in the non-coding RNA family, which has started to gain recognition after a decade of obscurity. The first couple of reports that emerged at the beginning of this decade and the amount of evidence that has accumulated thereafter has, however, encouraged RNA researchers to navigate further in the quest for the exploration of circular RNAs. The joining of 5′ and 3′ ends of RNA molecules through backsplicing forms circular RNAs during co-transcriptional or post-transcriptional processes. These molecules are capable of effectively sponging microRNAs, thereby regulating the cellular processes, as evidenced by numerous animal and plant systems. Preliminary studies have shown that circular RNA has an imperative role in transcriptional regulation and protein translation, and it also has significant therapeutic potential. The high stability of circular RNA is rendered by its closed ends; they are nevertheless prone to degradation by circulating endonucleases in serum or exosomes or by microRNA-mediated cleavage due to their high complementarity. However, the identification of circular RNAs involves diverse methodologies and the delineation of its possible role and mechanism in the regulation of cellular and molecular architecture has provided a new direction for the continuous research into circular RNA. In this review, we discuss the possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems.
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Affiliation(s)
- Ashirbad Guria
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Priyanka Sharma
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Sankar Natesan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
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21
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Pre-mRNA structures forming circular RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194410. [DOI: 10.1016/j.bbagrm.2019.194410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/25/2022]
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22
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Zhang P, Chao Z, Zhang R, Ding R, Wang Y, Wu W, Han Q, Li C, Xu H, Wang L, Xu Y. Circular RNA Regulation of Myogenesis. Cells 2019; 8:cells8080885. [PMID: 31412632 PMCID: PMC6721685 DOI: 10.3390/cells8080885] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/04/2019] [Accepted: 08/09/2019] [Indexed: 12/13/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of non-coding RNA generated by pre-mRNA back splicing, which is characterized by a closed-loop structure. Although circRNAs were firstly reported decades ago, their regulatory roles have not been discovered until recently. In this review, we discussed the putative biogenesis pathways and regulatory functions of circRNAs. Recent studies showed that circRNAs are abundant in skeletal muscle tissue, and their expression levels are regulated during muscle development and aging. We, thus, characterized the expression profile of circRNAs in skeletal muscle and discussed regulatory functions and mechanism-of-action of specific circRNAs in myogenesis. The future investigation into the roles of circRNAs in both physiological and pathological conditions may provide novel insights in skeletal muscle development and provide new therapeutic strategies for muscular diseases.
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Affiliation(s)
- Pengpeng Zhang
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Rui Zhang
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Ruoqi Ding
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Yaling Wang
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Wei Wu
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Qiu Han
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Cencen Li
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Haixia Xu
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Lei Wang
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China.
| | - Yongjie Xu
- Department of Biotechnology, College of Life Sciences, Xinyang Normal University, Xinyang 464000, China.
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23
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Circ-IGF1R has pro-proliferative and anti-apoptotic effects in HCC by activating the PI3K/AKT pathway. Gene 2019; 716:144031. [PMID: 31377314 DOI: 10.1016/j.gene.2019.144031] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Circular RNAs (circRNAs), a novel class of widespread and diverse endogenous RNAs, have been identified as critical regulators of various cancers, including hepatocellular carcinoma (HCC). However, the specific roles of circRNAs in HCC are largely unknown. In this study, we identified a novel circRNA, circ-IGF1R, in HCC tumour tissues and cell lines. Circ-IGF1R levels were found to be significantly upregulated in HCC tissues compared with levels in paired peritumoural tissues. The high expression levels of circ-IGF1R in HCC were associated with tumour size. Moreover, knocking down circ-IGF1R with siRNA significantly attenuated cell proliferation and induced cell apoptosis and cell cycle arrest in vitro. Further investigation revealed that PI3K/AKT signalling pathway activation was involved in the oncogenic functions of circ-IGF1R in HCC. Our study suggests that circ-IGF1R may be a potential target for the prevention and treatment of HCC.
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24
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Kölling M, Haddad G, Wegmann U, Kistler A, Bosakova A, Seeger H, Hübel K, Haller H, Mueller T, Wüthrich RP, Lorenzen JM. Circular RNAs in Urine of Kidney Transplant Patients with Acute T Cell-Mediated Allograft Rejection. Clin Chem 2019; 65:1287-1294. [PMID: 31371281 DOI: 10.1373/clinchem.2019.305854] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/01/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) have recently been described as novel noncoding regulators of gene expression. They are detectable in the blood of patients with acute kidney injury. We tested whether circRNAs were present in urine and could serve as new predictors of outcome in renal transplant patients with acute rejection. METHODS A global circRNA expression analysis using RNA from urine of patients with acute T cell-mediated renal allograft rejection and control transplant patients was performed. Dysregulated circRNAs were confirmed in a cohort of 62 patients with acute rejection, 10 patients after successful antirejection therapy, 18 control transplant patients without rejection, and 13 stable transplant patients with urinary tract infection. RESULTS A global screen revealed several circRNAs to be altered in urine of patients with acute rejection. Concentrations of 2 circRNAs including hsa_circ_0001334 and hsa_circ_0071475 were significantly increased. These were validated in the whole cohort of patients. hsa_circ_0001334 was upregulated in patients with acute rejection compared with controls. Concentrations of hsa_circ_0001334 normalized in patients with acute rejection following successful antirejection therapy. hsa_circ_0001334 was associated with higher decline in glomerular filtration rate 1 year after transplantation. CONCLUSIONS CircRNA concentrations are significantly dysregulated in patients with acute rejection at subclinical time points. Urinary hsa_circ_0001334 is a novel biomarker of acute kidney rejection, identifying patients with acute rejection and predicting loss of kidney function.
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Affiliation(s)
- Malte Kölling
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland;
| | - George Haddad
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Urs Wegmann
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | | | - Andrea Bosakova
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Harald Seeger
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Kerstin Hübel
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Hermann Haller
- Division of Nephrology and Hypertension, Hanover Medical School, Hanover, Germany
| | - Thomas Mueller
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Rudolf P Wüthrich
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland;
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25
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Czubak K, Taylor K, Piasecka A, Sobczak K, Kozlowska K, Philips A, Sedehizadeh S, Brook JD, Wojciechowska M, Kozlowski P. Global Increase in Circular RNA Levels in Myotonic Dystrophy. Front Genet 2019; 10:649. [PMID: 31428124 PMCID: PMC6689976 DOI: 10.3389/fgene.2019.00649] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/19/2019] [Indexed: 12/24/2022] Open
Abstract
Splicing aberrations induced as a consequence of the sequestration of muscleblind-like splicing factors on the dystrophia myotonica protein kinase transcript, which contains expanded CUG repeats, present a major pathomechanism of myotonic dystrophy type 1 (DM1). As muscleblind-like factors may also be important factors involved in the biogenesis of circular RNAs (circRNAs), we hypothesized that the level of circRNAs would be decreased in DM1. To test this hypothesis, we selected 20 well-validated circRNAs and analyzed their levels in several experimental systems (e.g., cell lines, DM muscle tissues, and a mouse model of DM1) using droplet digital PCR assays. We also explored the global level of circRNAs using two RNA-Seq datasets of DM1 muscle samples. Contrary to our original hypothesis, our results consistently showed a global increase in circRNA levels in DM1, and we identified numerous circRNAs that were increased in DM1. We also identified many genes (including muscle-specific genes) giving rise to numerous (>10) circRNAs. Thus, this study is the first to show an increase in global circRNA levels in DM1. We also provided preliminary results showing the association of circRNA level with muscle weakness and alternative splicing changes that are biomarkers of DM1 severity.
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Affiliation(s)
- Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Agnieszka Piasecka
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Katarzyna Kozlowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Saam Sedehizadeh
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J. David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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26
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Santer L, Bär C, Thum T. Circular RNAs: A Novel Class of Functional RNA Molecules with a Therapeutic Perspective. Mol Ther 2019; 27:1350-1363. [PMID: 31324392 DOI: 10.1016/j.ymthe.2019.07.001] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/26/2022] Open
Abstract
Circular RNAs (circRNAs) are a subclass of non-coding RNAs that lack free 3' and 5' ends and, thus, exist as continuous loop RNAs. Such circular transcripts have been identified for thousands of genes, are regulated in developmental stages and pathophysiological conditions, and are often expressed in a tissue- or cell-type-specific manner. For a long time, circular transcripts were considered as aberrant splicing by-products. However, high-throughput transcriptome sequencing and focused molecular characterization of individual circRNAs uncovered their ubiquity. Evidence emerges suggesting circRNAs are functional molecules. In this review, we illustrate the current knowledge of circRNA formation and circRNA detection methods. We summarize different molecular mechanisms of action and highlight circRNAs with specific roles in cardiovascular disease. Finally, we describe a number of tools for circRNA manipulation, which may be exploited for circRNA-based therapeutic interventions in the future.
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Affiliation(s)
- Laura Santer
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany.
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany; REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany; National Heart and Lung Institute, Imperial College London, London, UK.
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27
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Circular RNA circ-FoxO3 Inhibits Myoblast Cells Differentiation. Cells 2019; 8:cells8060616. [PMID: 31248210 PMCID: PMC6627427 DOI: 10.3390/cells8060616] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023] Open
Abstract
CircRNA is a type of closed circular non-coding RNA formed by reverse splicing and plays an important role in regulating the growth and development of plants and animals. To investigate the function of circ-FoxO3 in mouse myoblast cells' (C2C12) differentiation and proliferation, we used RT-qPCR to detect the expression level of circ-FoxO3 in mouse myoblast cells at different densities and different differentiation stages, and the specific interference fragment was used to inhibit the expression level of circ-FoxO3 in myoblast cells to observe its effect on myoblast cells proliferation and differentiation. We found that the expression level of circ-FoxO3 in myoblast cells increased with the prolongation of myoblast cells differentiation time, and its expression level decreased with the proliferation of myoblast cells. At the same time, we found that the differentiation ability of the cells was significantly increased (p < 0.05), but the cell proliferation was unchanged (p > 0.05) after inhibiting the expression of circ-FoxO3 in myoblast cells. Combining the results of bioinformatics analysis and the dual luciferase reporter experiment, we found that circ-FoxO3 is a sponge of miR-138-5p, which regulates muscle differentiation. Our study shows that circ-FoxO3 can inhibit the differentiation of C2C12 myoblast cells and lay a scientific foundation for further study of skeletal muscle development at circRNA levels.
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28
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Li J, Liu C. Coding or Noncoding, the Converging Concepts of RNAs. Front Genet 2019; 10:496. [PMID: 31178900 PMCID: PMC6538810 DOI: 10.3389/fgene.2019.00496] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of RNA. In this review, we summarize current evidence pointing to dual roles of RNA molecules defined by their coding and non-coding potentials. We also discuss how the emerging roles of RNA transform our understanding of gene expression and evolution.
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Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
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29
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30
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Long non-coding RNAs in vascular biology and disease. Vascul Pharmacol 2019; 114:13-22. [DOI: 10.1016/j.vph.2018.03.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 12/17/2022]
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Sekar S, Liang WS. Circular RNA expression and function in the brain. Noncoding RNA Res 2019; 4:23-29. [PMID: 30891534 PMCID: PMC6404376 DOI: 10.1016/j.ncrna.2019.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/04/2019] [Indexed: 01/16/2023] Open
Abstract
Within the last decade, active research on circular RNAs (circRNAs) has dramatically improved our understanding of the expression and function of these non-coding RNAs. While several mechanisms for circRNA function have been proposed, including sequestration of microRNAs and regulation of cellular proteins, studies provide evidence that circRNAs can regulate transcription and may also serve as biomarkers. Due to the heterogeneous nature of the brain, and the dynamic transcriptional mechanisms that support neurobiological pathways, the influence of circRNAs is potentially extensive. Understanding how circRNAs contribute to key neurological pathways will fill gaps in our understanding of brain function and provide valuable insight into novel therapeutic approaches to treat neurological diseases. Here, we review recent research on circRNA expression in the brain, describe the proposed functions of circRNAs, and evaluate the role of circRNAs in neurological diseases.
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Huda HA, Vijayarathna S, Oon CE, Chen Y, Kanwar JR, Ng ML, Sasidharan S. Functional Analysis of Circular RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1087:95-105. [PMID: 30259360 DOI: 10.1007/978-981-13-1426-1_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Circular RNAs characterize a class of widespread and diverse endogenous RNAs which are non-coding RNAs that are made by back-splicing events and have covalently closed loops with no polyadenylated tails. Various indications specify that circular RNAs (circRNAs) are plentiful in the human transcriptome. However, their participation in biological processes remains mostly undescribed. To date thousands of circRNAs have been revealed in organisms ranging from Drosophila melanogaster to Homo sapiens. Functional studies specify that these transcripts control expression of protein-coding linear transcripts and thus encompass a key component of gene expression regulation. This chapter provide a comprehensive overview on functional validation of circRNAs. Furthermore, we discuss the recent modern methodologies for the functional validation of circRNAs such as RNA interference (RNAi) gene silencing assay, luciferase reporter assays, circRNA gain-of-function investigation via overexpression of circular transcript assay, RT-q-PCR quantification, and other latest applicable assays. The methods described in this chapter are demonstrated on the cellular model.
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Affiliation(s)
- Hisham Alkatib Huda
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Soundararajan Vijayarathna
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Chern Ein Oon
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Yeng Chen
- Faculty of Dentistry, Dental Research & Training Unit, and Oral Cancer Research and Coordinating Centre (OCRCC), University of Malaya, Kuala Lumpur, Malaysia
| | - Jagat R Kanwar
- Faculty of Health, Nanomedicine-Laboratory of Immunology and Molecular Biomedical Research (LIMBR), School of Medicine (SoM), Deakin University, Geelong, VIC, Australia
| | - Mei Li Ng
- Integrative Medicine Cluster, Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Pulau Pinang, Malaysia.
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Genome-wide identification and functional analysis of circRNAs in Zea mays. PLoS One 2018; 13:e0202375. [PMID: 30533052 PMCID: PMC6289457 DOI: 10.1371/journal.pone.0202375] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/22/2018] [Indexed: 12/30/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs, which increasingly drawn researchers' attention in recent years as their importance in regulating gene expression at the transcriptional and post-transcriptional levels. With the development of high-throughput sequencing and bioinformatics, circRNAs have been widely analysed in animals, but the understanding of characteristics and function of circRNAs is limited in plants, especially in maize. Here, 3715 unique circRNAs were predicted in Zea mays systematically, and 8 of 12 circRNAs were validated by experiments. By analysing circRNA sequence, the events of alternative circularization phenomenon were found prevailed in maize. By comparing circRNAs in different species, it showed that part circRNAs are conserved across species, for example, there are 273 circRNAs conserved between maize and rice. Although most of the circRNAs have low expression levels, we found 149 differential expressed circRNAs responding to heat, cold, or drought, and 1782 tissue-specific expressed circRNAs. The results showed that those circRNAs may have potential biological functions in specific situations. Finally, two different methods were used to search circRNA functions, which were based on circRNAs originated from protein-coding genes and circRNAs as miRNA decoys. 346 circRNAs could act as miRNA decoys, which might modulate the effects of multiple molecular functions, including binding, catalytic activity, oxidoreductase activity, and transmembrane transporter activity. In summary, maize circRNAs were identified, classified and characterized systematically. We also explored circRNA functions, suggesting that circRNAs are involved in multiple molecular processes and play important roles in regulating of gene expression. Our results provide a rich resource for further study of maize circRNAs.
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Arnaiz E, Sole C, Manterola L, Iparraguirre L, Otaegui D, Lawrie CH. CircRNAs and cancer: Biomarkers and master regulators. Semin Cancer Biol 2018; 58:90-99. [PMID: 30550956 DOI: 10.1016/j.semcancer.2018.12.002] [Citation(s) in RCA: 269] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are a novel class of regulatory RNAs that despite being relatively abundant have only recently begun to be explored. There are many thousands of genes that appear capable of producing circRNAs, however the function of all but a handful remain to be determined. What is emerging about these highly conserved molecules is that they play important roles in biology and cancer biology in particular. The most explored function of circRNAs is as master regulators of gene expression that act to sequester or ´sponge´ other gene expression regulators, in particular miRNAs. They have also been demonstrated to function via direct modulation of transcription, and by interfering with splicing mechanisms. Although generally expressed in low abundance when compared to their linear counterparts, they are often expressed in a tissue- and developmental stage- specific manner. Coupled with their remarkable resistance to RNAse activity due to a covalent closed cyclic structure, circRNAs show great promise as novel biomarkers of cancer and other diseases. In this review we consider the current state of knowledge regarding these molecules, their synthesis, function, and association with cancer. We will also review some of the challenges that remain to be resolved if this emerging class of RNAs are really to become useful in the clinic.
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Affiliation(s)
- Esther Arnaiz
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n San Sebastián, 20014, Spain
| | - Carla Sole
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n San Sebastián, 20014, Spain
| | - Lorea Manterola
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n San Sebastián, 20014, Spain
| | - Leire Iparraguirre
- Multiple Sclerosis Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n San Sebastián, 20014, Spain
| | - David Otaegui
- Multiple Sclerosis Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n San Sebastián, 20014, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n San Sebastián, 20014, Spain; Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom; IKERBASQUE, Basque Foundation for Science, María Díaz Haroko Kalea, 3, 48013, Bilbao, Spain.
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35
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Wilusz JE. A 360° view of circular RNAs: From biogenesis to functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1478. [PMID: 29655315 PMCID: PMC6002912 DOI: 10.1002/wrna.1478] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022]
Abstract
The first circular RNA (circRNA) was identified more than 40 years ago, but it was only recently appreciated that circRNAs are common outputs of many eukaryotic protein-coding genes. Some circRNAs accumulate to higher levels than their associated linear mRNAs, especially in the nervous system, and have clear regulatory functions that result in organismal phenotypes. The pre-mRNA splicing machinery generates circRNAs via backsplicing reactions, which are often facilitated by intronic repeat sequences that base pair to one another and bring the intervening splice sites into close proximity. When spliceosomal components are limiting, circRNAs can become the preferred gene output, and backsplicing reactions are further controlled by exon skipping events and the combinatorial action of RNA binding proteins. This allows circRNAs to be expressed in a tissue- and stage-specific manner. Once generated, circRNAs are highly stable transcripts that often accumulate in the cytoplasm. The functions of most circRNAs remain unknown, but some can regulate the activities of microRNAs or be translated to produce proteins. Circular RNAs can further interface with the immune system as well as control gene expression events in the nucleus, including alternative splicing decisions. Circular RNAs thus represent a large class of RNA molecules that are tightly regulated, and it is becoming increasingly clear that they likely impact many biological processes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA.
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Affiliation(s)
- Jeremy E. Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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36
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Kölling M, Seeger H, Haddad G, Kistler A, Nowak A, Faulhaber-Walter R, Kielstein J, Haller H, Fliser D, Mueller T, Wüthrich RP, Lorenzen JM. The Circular RNA ciRs-126 Predicts Survival in Critically Ill Patients With Acute Kidney Injury. Kidney Int Rep 2018; 3:1144-1152. [PMID: 30197981 PMCID: PMC6127441 DOI: 10.1016/j.ekir.2018.05.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/09/2018] [Accepted: 05/28/2018] [Indexed: 02/08/2023] Open
Abstract
Introduction Circular RNAs (circRNAs) have recently been described as novel noncoding regulators of gene expression. They might have an impact on microRNA expression by their sponging activity. The detectability in blood of these RNA transcripts has been demonstrated in patients with cancer and cardiovascular disease. We tested the hypothesis that circulating circRNAs in blood of critically ill patients with acute kidney injury (AKI) at inception of renal replacement therapy may also be dysregulated and associated with patient survival. Methods We performed a global circRNA expression analysis using RNA isolated from blood of patients with AKI as well as controls. This global screen revealed several dysregulated circRNAs in patients with AKI. Most highly increased circRNA-array−based transcripts as well as expression of the circRNA target miR-126-5p were confirmed in blood of 109 patients with AKI, 30 age-matched healthy controls, 25 critically ill non-AKI patients, and 20 patients on maintenance hemodialysis by quantitative real-time polymerase chain reaction. Results Circulating concentrations of 3 novel circRNAs were amplified in blood of patients with AKI and in controls. Circular RNA sponge of miR-126 (or ciRs-126) was most highly altered compared to healthy controls and disease controls (fold change of 52.1). ciRs-126 was shown to bioinformatically sponge miR-126-5p, which was found to be highly suppressed in AKI patients and hypoxic endothelial cells. Cox regression and Kaplan−Meier curve analysis revealed ciRs-126 as an independent predictor of 28-day survival (P < 0.01). Conclusion Circulating concentrations of circRNAs in patients with AKI are detectable. ciRs-126 may potentially sponge miR-126-5p and acts as a predictor of mortality in this patient cohort.
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Affiliation(s)
- Malte Kölling
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Harald Seeger
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - George Haddad
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | | | - Albina Nowak
- Department of Internal Medicine, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Robert Faulhaber-Walter
- Department of Medicine, Division of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Jan Kielstein
- Department of Medicine, Division of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Hermann Haller
- Department of Medicine, Division of Nephrology and Hypertension, Hannover Medical School, Hannover, Germany
| | - Danilo Fliser
- Saarland University Medical Centre, Homburg/Saar, Germany
| | - Thomas Mueller
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Rudolf P Wüthrich
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
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37
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Dragomir M, Calin GA. Circular RNAs in Cancer - Lessons Learned From microRNAs. Front Oncol 2018; 8:179. [PMID: 29911069 PMCID: PMC5992376 DOI: 10.3389/fonc.2018.00179] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/08/2018] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNA) are RNA molecules built from fragments of linear pre-messenger RNAs and other linear RNA species through a process termed "back-splicing" in which the 3' and 5' ends are joined together giving rise to a covalently uninterrupted loop. circRNAs are not new members of the RNA world; they were first discovered in the early 1990s. The novelty is their abundance in the mammalian cells, as recently thousands of circRNAs were discovered and annotated. The biogenesis of circRNAs is a partially characterized process, regulated by three different mechanisms: exon skipping, intron pairing, and RNA-binding proteins. On the other hand, the function of circRNAs remains largely unknown and only a handful of singular reports describe in detail the biological roles of some circular transcripts. In a very short period of time, numerous circRNAs were associated with various cancer types and were also identified in bodily fluids with the potential of being disease-specific biomarkers. In this review, we briefly describe the biogenesis and function of circRNAs and present the circular transcripts that were more than once reported in literature to be associated with cancer. Finally, we point out some of the difficulties encountered in the study of circRNAs in cancer, as we consider that taking these into account could accelerate and improve our understanding of the biologic and translational use of circRNAs in human diseases.
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Affiliation(s)
- Mihnea Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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38
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Lei K, Bai H, Wei Z, Xie C, Wang J, Li J, Chen Q. The mechanism and function of circular RNAs in human diseases. Exp Cell Res 2018; 368:147-158. [PMID: 29730164 DOI: 10.1016/j.yexcr.2018.05.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are a recently discovered form of RNA. Initially, circRNAs were believed to result from errors during the process of gene transcription. However, after further investigation, scientists suggested that circRNAs are of great biological significance. CircRNAs show stability, conservation, abundance, and tissue and stage specificity. They can also function as miRNA sponges, regulate gene expression, and interact with proteins to affect cell behavior. Emerging evidence has also demonstrated that circRNAs participate or show abnormal expression in diseases, including central nervous system diseases, cardiovascular diseases and cancers, indicating their marked potential in the prediction and prognosis of diseases and clinical treatment.
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Affiliation(s)
- Kexin Lei
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hetian Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zihao Wei
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Changqing Xie
- Xiangya Stomatological Hospital, Central South University, Changsha, China
| | - Jiongke Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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39
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Holdt LM, Kohlmaier A, Teupser D. Molecular roles and function of circular RNAs in eukaryotic cells. Cell Mol Life Sci 2018; 75:1071-1098. [PMID: 29116363 PMCID: PMC5814467 DOI: 10.1007/s00018-017-2688-5] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/29/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022]
Abstract
Protein-coding and noncoding genes in eukaryotes are typically expressed as linear messenger RNAs, with exons arranged colinearly to their genomic order. Recent advances in sequencing and in mapping RNA reads to reference genomes have revealed that thousands of genes express also covalently closed circular RNAs. Many of these circRNAs are stable and contain exons, but are not translated into proteins. Here, we review the emerging understanding that both, circRNAs produced by co- and posttranscriptional head-to-tail "backsplicing" of a downstream splice donor to a more upstream splice acceptor, as well as circRNAs generated from intronic lariats during colinear splicing, may exhibit physiologically relevant regulatory functions in eukaryotes. We describe how circRNAs impact gene expression of their host gene locus by affecting transcriptional initiation and elongation or splicing, and how they partake in controlling the function of other molecules, for example by interacting with microRNAs and proteins. We conclude with an outlook how circRNA dysregulation affects disease, and how the stability of circRNAs might be exploited in biomedical applications.
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Affiliation(s)
- Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| | - Alexander Kohlmaier
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
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40
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Ouyang H, Chen X, Wang Z, Yu J, Jia X, Li Z, Luo W, Abdalla BA, Jebessa E, Nie Q, Zhang X. Circular RNAs are abundant and dynamically expressed during embryonic muscle development in chickens. DNA Res 2017; 25:71-86. [PMID: 29036326 PMCID: PMC5824844 DOI: 10.1093/dnares/dsx039] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 09/07/2017] [Indexed: 12/13/2022] Open
Abstract
The growth and development of skeletal muscle is regulated by proteins as well as non-coding RNAs. Circular RNAs (circRNAs) are universally expressed in various tissues and cell types, and regulate gene expression in eukaryotes. To identify the circRNAs during chicken embryonic skeletal muscle development, leg muscles of female Xinghua (XH) chicken at three developmental time points 11 embryo age (E11), 16 embryo age (E16) and 1 day post hatch (P1) were performed RNA sequencing. We identified 13,377 circRNAs with 3,036 abundantly expressed and most were derived from coding exons. A total of 462 differentially expressed circRNAs were identified (fold change > 2; q-value < 0.05). Parental genes of differentially expressed circRNAs were related to muscle biological processes. There were 946 exonic circRNAs have been found that harbored one or more miRNA-binding site for 150 known miRNAs. We validated that circRBFOX2s promoted cell proliferation through interacted with miR-206. These data collectively indicate that circRNAs are abundant and dynamically expressed during embryonic muscle development and could play key roles through sequestering miRNAs as well as other functions.
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Affiliation(s)
- Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Xiaolan Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Zhijun Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Jiao Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Xinzheng Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Wei Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Bahareldin Ali Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Endashaw Jebessa
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, People's Republic of China
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Tan WLW, Lim BTS, Anene-Nzelu CGO, Ackers-Johnson M, Dashi A, See K, Tiang Z, Lee DP, Chua WW, Luu TDA, Li PYQ, Richards AM, Foo RSY. A landscape of circular RNA expression in the human heart. Cardiovasc Res 2017; 113:298-309. [PMID: 28082450 DOI: 10.1093/cvr/cvw250] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/06/2016] [Indexed: 12/17/2022] Open
Abstract
Aims Circular RNA (circRNA) is a newly validated class of single-stranded RNA, ubiquitously expressed in mammalian tissues and possessing key functions including acting as microRNA sponges and as transcriptional regulators by binding to RNA-binding proteins. While independent studies confirm the expression of circRNA in various tissue types, genome-wide circRNA expression in the heart has yet to be described in detail. Methods and results We performed deep RNA-sequencing on ribosomal-depleted RNA isolated from 12 human hearts, 25 mouse hearts and across a 28-day differentiation time-course of human embryonic stem cell-derived cardiomyocytes. Using purpose-designed bioinformatics tools, we uncovered a total of 15 318 and 3017 cardiac circRNA within human and mouse, respectively. Their abundance generally correlates with the abundance of their cognate linear RNA, but selected circRNAs exist at disproportionately higher abundance. Top highly expressed circRNA corresponded to key cardiac genes including Titin (TTN), RYR2, and DMD. The most abundant cardiac-expressed circRNA is a cytoplasmic localized single-exon circSLC8A1-1. The longest human transcript TTN alone generates up to 415 different exonic circRNA isoforms, the majority (83%) of which originates from the I-band domain. Finally, we confirmed the expression of selected cardiac circRNA by RT-PCR, Sanger sequencing and single molecule RNA-fluorescence in situ hybridization. Conclusions Our data provide a detailed circRNA expression landscape in hearts. There is a high-abundance of specific cardiac-expressed circRNA. These findings open up a new avenue for future investigation into this emerging class of RNA.
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Affiliation(s)
- Wilson L W Tan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Benson T S Lim
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Chukwuemeka G O Anene-Nzelu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Matthew Ackers-Johnson
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Albert Dashi
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Kelvin See
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Zenia Tiang
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Dominic Paul Lee
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Wee Woon Chua
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Tuan D A Luu
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Peter Y Q Li
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Arthur Mark Richards
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
| | - Roger S Y Foo
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.,Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, 14 Medical Drive, Singapore 117599, Singapore
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Abstract
Just a few years ago, it had been assumed that the dominant RNA isoforms produced from eukaryotic genes were variants of messenger RNA, functioning as intermediates in gene expression. In early 2012, however, a surprising discovery was made: circular RNA (circRNA) was shown to be a transcriptional product in thousands of human and mouse genes and in hundreds of cases constituted the dominant RNA isoform. Subsequent studies revealed that the expression of circRNAs is developmentally regulated, tissue and cell-type specific, and shared across the eukaryotic tree of life. These features suggest important functions for these molecules. Here, we describe major advances in the field of circRNA biology, focusing on the regulation of and functional roles played by these molecules.
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Affiliation(s)
- Steven P Barrett
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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43
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Li M, Ding W, Sun T, Tariq MA, Xu T, Li P, Wang J. Biogenesis of circular RNAs and their roles in cardiovascular development and pathology. FEBS J 2017; 285:220-232. [PMID: 28783257 DOI: 10.1111/febs.14191] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/10/2017] [Accepted: 08/03/2017] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are a newly discovered type of RNA generated by back-splicing of precursor mRNA and found in many species. They are, expressed in a tissue-specific manner and fulfill regulatory activities in many biological processes. Recent research has revealed that circRNAs play critical roles in the development and pathologies of the cardiovascular system. Some of these circRNAs show aberrant expression and regulatory activities during heart disease including heart failure and cardiac infarction and hypertrophy. These findings suggest that circRNAs might be a suitable target for the treatment and prevention of heart disease. In this review, we summarize the latest research on the biogenesis and functions of circRNAs with emphasis on the regulatory roles of circRNAs in the development and pathologies of the cardiovascular system.
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Affiliation(s)
- Mengyang Li
- Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, China
| | - Wei Ding
- Department of Comprehensive Internal Medicine, Affiliated Hospital, Qingdao University, China
| | - Teng Sun
- Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, China
| | - Muhammad A Tariq
- Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, China
| | - Tao Xu
- Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, China
| | - Peifeng Li
- Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, China
| | - Jianxun Wang
- Center for Regenerative Medicine, Institute for Translational Medicine, Qingdao University, China
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44
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Dou Y, Li S, Yang W, Liu K, Du Q, Ren G, Yu B, Zhang C. Genome-wide Discovery of Circular RNAs in the Leaf and Seedling Tissues of Arabidopsis Thaliana. Curr Genomics 2017; 18:360-365. [PMID: 29081691 PMCID: PMC5635619 DOI: 10.2174/1389202918666170307161124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/12/2016] [Accepted: 10/27/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Recently, identification and functional studies of circular RNAs, a type of non-coding RNAs arising from a ligation of 3' and 5' ends of a linear RNA molecule, were conducted in mammalian cells with the development of RNA-seq technology. METHOD Since compared with animals, studies on circular RNAs in plants are less thorough, a genome-wide identification of circular RNA candidates in Arabidopsis was conducted with our own developed bioinformatics tool to several existing RNA-seq datasets specifically for non-coding RNAs. RESULTS A total of 164 circular RNA candidates were identified from RNA-seq data, and 4 circular RNA transcripts, including both exonic and intronic circular RNAs, were experimentally validated. Interestingly, our results show that circular RNA transcripts are enriched in the photosynthesis system for the leaf tissue and correlated to the higher expression levels of their parent genes. Sixteen out of all 40 genes that have circular RNA candidates are related to the photosynthesis system, and out of the total 146 exonic circular RNA candidates, 63 are found in chloroplast.
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Affiliation(s)
- Yongchao Dou
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Shengjun Li
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Weilong Yang
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Kan Liu
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Qian Du
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology and Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Yu
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
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45
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Abstract
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases. We conclude with a discussion of the current experimental progress on the topic.
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46
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Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, Wyler E, Perez-Hernandez D, Ramberger E, Shenzis S, Samson M, Dittmar G, Landthaler M, Chekulaeva M, Rajewsky N, Kadener S. Translation of CircRNAs. Mol Cell 2017; 66:9-21.e7. [PMID: 28344080 PMCID: PMC5387669 DOI: 10.1016/j.molcel.2017.02.021] [Citation(s) in RCA: 1243] [Impact Index Per Article: 177.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 01/04/2017] [Accepted: 02/21/2017] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry. Next, by performing in vivo and in vitro translation assays, we show that UTRs of ribo-circRNAs (cUTRs) allow cap-independent translation. Moreover, we found that starvation and FOXO likely regulate the translation of a circMbl isoform. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.
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Affiliation(s)
- Nagarjuna Reddy Pamudurti
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Osnat Bartok
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Christin Stottmeister
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Larissa Ruhe
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Mor Hanan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Emanuel Wyler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Daniel Perez-Hernandez
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Evelyn Ramberger
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Shlomo Shenzis
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Moshe Samson
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gunnar Dittmar
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Marina Chekulaeva
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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47
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Circular RNA 0000096 affects cell growth and migration in gastric cancer. Br J Cancer 2017; 116:626-633. [PMID: 28081541 PMCID: PMC5344286 DOI: 10.1038/bjc.2016.451] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 01/17/2023] Open
Abstract
Background: Circular RNAs (circRNAs) are a class of non-coding RNAs broadly expressed in cells of various species. Their role in cancers, especially in gastric cancer, is poorly understood. Methods: Circular RNA 0000096 (hsa_circ_0000096) levels in 101 paired gastric cancer tissues and adjacent non-tumorous tissues from patients with gastric cancer were detected by real-time quantitative reverse transcription-polymerase chain reaction. A receiver operating characteristic curve was generated to evaluate the diagnostic value of hsa_circ_0000096. RNA interference was used to manipulate the expression of hsa_circ_0000096. Its biological effects were evaluated by flow cytometry, real-time cell analysis, a wound scratch assay, western blot analysis and xenograft models. Results: Hsa_circ_0000096 was found to be significantly downregulated in gastric cancer tissues and gastric cancer cell lines compared with paired adjacent non-tumorous tissues and normal gastric epithelial cells (P<0.001). Moreover, knockdown of hsa_circ_0000096 significantly inhibited cell proliferation and migration in vitro and in vivo. The results of both immunohistochemical and western blot analyses showed that the protein levels of cyclin D1, cyclin-dependent kinase 6 (CDK6), matrix metalloproteinase-2 and MMP-9 were significantly reduced in vitro and in vivo. A gastric cancer xenograft nude mouse model indicated that Ki67 and VEGF were reduced in a dose-dependent manner following knockdown of hsa_circ_0000096. However, the expression of E-cadherin increased. Conclusions: Hsa_circ_0000096 may be used as a potential novel biomarker for gastric cancer. It affects gastric cancer cell growth and migration by regulating cyclin D1, CDK6, MMP-2 and MMP-9.
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48
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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49
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Abstract
Pre-mRNAs from thousands of eukaryotic genes can be non-canonically spliced to generate circular RNAs, some of which accumulate to higher levels than their associated linear mRNA. Recent work has revealed widespread mechanisms that dictate whether the spliceosome generates a linear or circular RNA. For most genes, circular RNA biogenesis via backsplicing is far less efficient than canonical splicing, but circular RNAs can accumulate due to their long half-lives. Backsplicing is often initiated when complementary sequences from different introns base pair and bring the intervening splice sites close together. This process is further regulated by the combinatorial action of RNA binding proteins, which allow circular RNAs to be expressed in unique patterns. Some genes do not require complementary sequences to generate RNA circles and instead take advantage of exon skipping events. It is still unclear what most mature circular RNAs do, but future investigations into their functions will be facilitated by recently described methods to modulate circular RNA levels.
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Affiliation(s)
- Jeremy E Wilusz
- a Department of Biochemistry and Biophysics , University of Pennsylvania Perelman School of Medicine , PA , USA
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50
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Characterization of circular RNAs in human, mouse and rat hearts. J Mol Cell Cardiol 2016; 98:103-7. [PMID: 27476877 DOI: 10.1016/j.yjmcc.2016.07.007] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 11/21/2022]
Abstract
Deep sequencing techniques and advanced data analysis methods recently enabled the characterization of thousands of circular RNA isoforms (circRNAs) from a number of tissues and organisms. There is emerging evidence that some circRNAs may have important biological functions or serve as diagnostic biomarkers in disease conditions. In order to analyze circRNA expression in the heart and its changes in different conditions we performed RNA-Seq analysis of ribosome-depleted libraries from rats (neonatal and adult), mice (sham or after transverse aortic constriction, TAC) and humans (failing, non-failing). All samples were sequenced after treatment with exonuclease RNase R or a mock treatment and >9000 candidate circRNAs were detected for each species. Additionally, we performed separate isolation of nuclear and cytoplasmic RNA and co-immunoprecipitated RNA interacting with endogenous argonaute 2 (Ago2) in primary cardiac myocytes. We found circRNAs to be significantly enriched in the cytoplasm compared to linear transcripts and to have a similar level of association with Ago2. Notably in all three species we observed dozens of circRNAs arising from the titin (Ttn) gene, which is known to undergo highly complex alternative splicing during heart maturation. Correspondingly we observed extensive differential regulation of Ttn circRNAs between neonatal and adult rat hearts, suggesting that circRNA formation could be involved in the regulation of titin splicing. We expect that our inventory of cardiac circRNAs, as well as the information on their conservation and differential expression will provide an important basis for further studies addressing their function and suitability as biomarkers.
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