1
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Zhang B, Zhang H, Wang Z, Cao H, Zhang N, Dai Z, Liang X, Peng Y, Wen J, Zhang X, Zhang L, Luo P, Zhang J, Liu Z, Cheng Q, Peng R. The regulatory role and clinical application prospects of circRNA in the occurrence and development of CNS tumors. CNS Neurosci Ther 2024; 30:e14500. [PMID: 37953502 PMCID: PMC11017455 DOI: 10.1111/cns.14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Central nervous system (CNS) tumors originate from the spinal cord or brain. The study showed that even with aggressive treatment, malignant CNS tumors have high mortality rates. However, CNS tumor risk factors and molecular mechanisms have not been verified. Due to the reasons mentioned above, diagnosis and treatment of CNS tumors in clinical practice are currently fraught with difficulties. Circular RNAs (circRNAs), single-stranded ncRNAs with covalently closed continuous structures, are essential to CNS tumor development. Growing evidence has proved the numeral critical biological functions of circRNAs for disease progression: sponging to miRNAs, regulating gene transcription and splicing, interacting with proteins, encoding proteins/peptides, and expressing in exosomes. AIMS This review aims to summarize current progress regarding the molecular mechanism of circRNA in CNS tumors and to explore the possibilities of clinical application based on circRNA in CNS tumors. METHODS We have summarized studies of circRNA in CNS tumors in Pubmed. RESULTS This review summarized their connection with CNS tumors and their functions, biogenesis, and biological properties. Furthermore, we introduced current advances in clinical RNA-related technologies. Then we discussed the diagnostic and therapeutic potential (especially for immunotherapy, chemotherapy, and radiotherapy) of circRNA in CNS tumors in the context of the recent advanced research and application of RNA in clinics. CONCLUSIONS CircRNA are increasingly proven to participate in decveloping CNS tumors. An in-depth study of the causal mechanisms of circRNAs in CNS tomor progression will ultimately advance their implementation in the clinic and developing new strategies for preventing and treating CNS tumors.
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Affiliation(s)
- Bo Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Hao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Department of Neurosurgery, The Second Affiliated HospitalChongqing Medical UniversityChongqingChina
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- MRC Centre for Regenerative Medicine, Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Hui Cao
- Department of Psychiatry, The School of Clinical MedicineHunan University of Chinese MedicineChangshaChina
| | - Nan Zhang
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xisong Liang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yun Peng
- Teaching and Research Section of Clinical NursingXiangya Hospital of Central South UniversityChangshaChina
- Department of Geriatrics, Xiangya HospitalCentral South UniversityChangshaChina
| | - Jie Wen
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xun Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Renjun Peng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
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2
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Song B, Qian J, Fu J. Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine. Int J Legal Med 2024; 138:329-350. [PMID: 37770641 DOI: 10.1007/s00414-023-03091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.
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Affiliation(s)
- Binghui Song
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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3
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Barbosa DF, Oliveira LS, Nachtigall PG, Valentini Junior R, de Souza N, Paschoal AR, Kashiwabara AY. cirCodAn: A GHMM-based tool for accurate prediction of coding regions in circRNA. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:289-334. [PMID: 38448139 DOI: 10.1016/bs.apcsb.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Studies focusing on characterizing circRNAs with the potential to translate into peptides are quickly advancing. It is helping to elucidate the roles played by circRNAs in several biological processes, especially in the emergence and development of diseases. While various tools are accessible for predicting coding regions within linear sequences, none have demonstrated accurate open reading frame detection in circular sequences, such as circRNAs. Here, we present cirCodAn, a novel tool designed to predict coding regions in circRNAs. We evaluated the performance of cirCodAn using datasets of circRNAs with strong translation evidence and showed that cirCodAn outperformed the other tools available to perform a similar task. Our findings demonstrate the applicability of cirCodAn to identify coding regions in circRNAs, which reveals the potential of use of cirCodAn in future research focusing on elucidating the biological roles of circRNAs and their encoded proteins. cirCodAn is freely available at https://github.com/denilsonfbar/cirCodAn.
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Affiliation(s)
- Denilson Fagundes Barbosa
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de Santa Catarina (IFSC), Canoinhas, Santa Catarina, Brazil
| | - Liliane Santana Oliveira
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rodolpho Valentini Junior
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Nayane de Souza
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Alexandre Rossi Paschoal
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - André Yoshiaki Kashiwabara
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil.
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4
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Wang L, Cui X, Jiang F, Hu Y, Wan W, Li G, Lin Y, Xiao J. Circular RNA Translation in Cardiovascular Diseases. Curr Genomics 2023; 24:66-71. [PMID: 37994328 PMCID: PMC10662380 DOI: 10.2174/1389202924666230911121358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 11/24/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous functional RNA generated by back-splicing. Recently, circRNAs have been found to have certain coding potential. Proteins/peptides translated from circRNAs play essential roles in various diseases. Here, we briefly summarize the basic knowledge and technologies that are usually applied to study circRNA translation. Then, we focus on the research progress of circRNA translation in cardiovascular diseases and discuss the perspective and future direction of translatable circRNA study in cardiovascular diseases.
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Affiliation(s)
- Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Xinxin Cui
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Fei Jiang
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Yuxue Hu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Wensi Wan
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Yanjuan Lin
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
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5
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Lindner G, Takenaka K, Santucci K, Gao Y, Janitz M. Protein-coding circular RNAs - mechanism, detection, and their role in cancer and neurodegenerative diseases. Biochem Biophys Res Commun 2023; 678:68-77. [PMID: 37619313 DOI: 10.1016/j.bbrc.2023.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Circular RNAs (circRNAs) are a unique class of non-coding RNAs and were originally thought to have no protein-coding potential due to their lack of a 5' cap and 3' poly(A) tail. However, recent studies have challenged this notion and revealed that some circRNAs have protein-coding potential. They have emerged as a key area of interest in cancer and neurodegeneration research as recent studies have identified several circRNAs that can produce functional proteins with important roles in cancer progression. The protein-coding potential of circRNAs is determined by the presence of an open reading frame (ORF) within the circular structure that can encode a protein. In some cases, the ORF can be translated into a functional protein despite the lack of traditional mRNA features. While the protein-coding potential of most circRNAs remains unclear, several studies have identified specific circRNAs that can produce functional proteins. Understanding the protein-coding potential of circRNAs is important for unravelling their biological functions and potential roles in disease. Our review provides comprehensive coverage of recent advances in the field of circRNA protein-coding capacity and its impact on cancer and neurodegenerative diseases pathogenesis and progression.
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Affiliation(s)
- Grace Lindner
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kristina Santucci
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yulan Gao
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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6
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Hwang JY, Kook TL, Paulus SM, Park JW. Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches. Curr Bioinform 2023; 19:3-13. [PMID: 38500957 PMCID: PMC10947221 DOI: 10.2174/1574893618666230505101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/09/2023] [Accepted: 03/16/2023] [Indexed: 03/20/2024]
Abstract
Over the past two decades, studies have discovered a special form of alternative splicing (AS) that produces a circular form of RNA. This stands in contrast to normal AS, which produces a linear form of RNA. Although these circRNAs have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of these studies has been on the regulatory role of circRNAs with the assumption that circRNAs are non-coding. As non-coding RNAs, they may regulate mRNA transcription, tumor initiation, and translation by sponging miRNAs and RNA-binding proteins (RBPs). In addition to these regulatory roles of circRNAs, however, recent studies have provided strong evidence for their translation. The translation of circRNAs is expected to have an important role in promoting cancer cell growth and activating molecular pathways related to cancer development. In some cases, the translation of circRNAs is shown to be efficiently driven by an internal ribosome entry site (IRES). The development of a computational tool for identifying and characterizing the translation of circRNAs using high-throughput sequencing and IRES increases identifiable proteins translated from circRNAs. In turn, it has a substantial impact on helping researchers understand the functional role of proteins derived from circRNAs. New web resources for aggregating, cataloging, and visualizing translational information of circRNAs derived from previous studies have been developed. In this paper, general concepts of circRNA, circRNA biogenesis, translation of circRNA, and existing circRNA tools and databases are summarized to provide new insight into circRNA studies.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Tae Lim Kook
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Sydney M. Paulus
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Juw Won Park
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
- CIEHS Biostatistics and Informatics Facility Core, University of Louisville, Louisville, KY 40292, USA
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7
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Jing T, Wu Y, Wan A, Ge C, Chen ZJ, Du Y. Circular RNA as a Novel Regulator and Promising Biomarker in Polycystic Ovary Syndrome. Biomolecules 2023; 13:1101. [PMID: 37509138 PMCID: PMC10377156 DOI: 10.3390/biom13071101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/09/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent metabolic and reproductive disorder that causes low fertility in females. Despite its detrimental effects on women's health, care for PCOS has been impeded by its undefined pathogenesis. Thus, there is an urgent need to explore novel biomarkers and therapeutic targets for the diagnosis and treatment of PCOS. Circular RNAs (circRNAs) are a class of noncoding RNAs with covalently closed cyclic structures, present in high abundance, and show development-stage specific expression patterns. Recent studies have demonstrated that circRNAs participate in PCOS progression by modulating various biological functions, including cell proliferation, apoptosis, and steroidogenesis. In addition, circRNAs are widely present in the follicular fluid of women with PCOS, indicating their potential as diagnostic biomarkers and therapeutic targets for PCOS. This review provides the current knowledge of circRNAs in PCOS, including their regulatory functions and molecular mechanisms, and explores their potential as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Tianrui Jing
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Yifan Wu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Anran Wan
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Chengmin Ge
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250012, China
- NMU-SD Suzhou Collaborative Innovation Center for Reproductive Medicine, Suzhou 215000, China
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
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8
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Hu F, Peng Y, Fan X, Zhang X, Jin Z. Circular RNAs: implications of signaling pathways and bioinformatics in human cancer. Cancer Biol Med 2023; 20:j.issn.2095-3941.2022.0466. [PMID: 36861443 PMCID: PMC9978890 DOI: 10.20892/j.issn.2095-3941.2022.0466] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Circular RNAs (circRNAs) form a class of endogenous single-stranded RNA transcripts that are widely expressed in eukaryotic cells. These RNAs mediate post-transcriptional control of gene expression and have multiple functions in biological processes, such as transcriptional regulation and splicing. They serve predominantly as microRNA sponges, RNA-binding proteins, and templates for translation. More importantly, circRNAs are involved in cancer progression, and may serve as promising biomarkers for tumor diagnosis and therapy. Although traditional experimental methods are usually time-consuming and laborious, substantial progress has been made in exploring potential circRNA-disease associations by using computational models, summarized signaling pathway data, and other databases. Here, we review the biological characteristics and functions of circRNAs, including their roles in cancer. Specifically, we focus on the signaling pathways associated with carcinogenesis, and the status of circRNA-associated bioinformatics databases. Finally, we explore the potential roles of circRNAs as prognostic biomarkers in cancer.
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Affiliation(s)
- Fan Hu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Yin Peng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Xinmin Fan
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Xiaojing Zhang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
- Correspondence to: Zhe Jin and Xiaojing Zhang, E-mail: and
| | - Zhe Jin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, School of Basic Medical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
- Correspondence to: Zhe Jin and Xiaojing Zhang, E-mail: and
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9
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Liu R, Ma Y, Guo T, Li G. Identification, biogenesis, function, and mechanism of action of circular RNAs in plants. PLANT COMMUNICATIONS 2023; 4:100430. [PMID: 36081344 PMCID: PMC9860190 DOI: 10.1016/j.xplc.2022.100430] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.
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Affiliation(s)
- Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Yu Ma
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
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10
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Ruan H, Wang PC, Han L. Characterization of circular RNAs with advanced sequencing technologies in human complex diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1759. [PMID: 36164985 DOI: 10.1002/wrna.1759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/09/2022] [Accepted: 08/02/2022] [Indexed: 01/31/2023]
Abstract
Circular RNAs (circRNAs) are one category of non-coding RNAs that do not possess 5' caps and 3' free ends. Instead, they are derived in closed circle forms from pre-mRNAs by a non-canonical splicing mechanism named "back-splicing." CircRNAs were discovered four decades ago, initially called "scrambled exons." Compared to linear RNAs, the expression levels of circRNAs are considerably lower, and it is challenging to identify circRNAs specifically. Thus, the biological relevance of circRNAs has been underappreciated until the advancement of next generation sequencing (NGS) technology. The biological insights of circRNAs, such as their tissue-specific expression patterns, biogenesis factors, and functional effects in complex diseases, namely human cancers, have been extensively explored in the last decade. With the invention of the third generation sequencing (TGS) with longer sequencing reads and newly designed strategies to characterize full-length circRNAs, the panorama of circRNAs in human complex diseases could be further unveiled. In this review, we first introduce the history of circular RNA detection. Next, we describe widely adopted NGS-based methods and the recently established TGS-based approaches capable of characterizing circRNAs in full-length. We then summarize data resources and representative circRNA functional studies related to human complex diseases. In the last section, we reviewed computational tools and discuss the potential advantages of utilizing advanced sequencing approaches to a functional interpretation of full-length circRNAs in complex diseases. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Hang Ruan
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Peng-Cheng Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, USA.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
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11
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Yang J, Liu M, Fang X, Zhang H, Ren Q, Zheng Y, Wang Y, Zhou Y. Advances in peptides encoded by non-coding RNAs: A cargo in exosome. Front Oncol 2022; 12:1081997. [PMID: 36620552 PMCID: PMC9822543 DOI: 10.3389/fonc.2022.1081997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.
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Affiliation(s)
- Jing Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengxiao Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xidong Fang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qian Ren
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
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12
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Samarfard S, Ghorbani A, Karbanowicz TP, Lim ZX, Saedi M, Fariborzi N, McTaggart AR, Izadpanah K. Regulatory non-coding RNA: The core defense mechanism against plant pathogens. J Biotechnol 2022; 359:82-94. [PMID: 36174794 DOI: 10.1016/j.jbiotec.2022.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.
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Affiliation(s)
- Samira Samarfard
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, the Islamic Republic of Iran.
| | | | - Zhi Xian Lim
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mahshid Saedi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, the Islamic Republic of Iran
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, the Islamic Republic of Iran
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Keramatollah Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, the Islamic Republic of Iran
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13
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Cao Z, Li G. MStoCIRC: A powerful tool for downstream analysis of MS/MS data to predict translatable circRNAs. Front Mol Biosci 2022; 9:791797. [PMID: 36072432 PMCID: PMC9441560 DOI: 10.3389/fmolb.2022.791797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
CircRNAs are formed by a non-canonical splicing method and appear circular in nature. CircRNAs are widely distributed in organisms and have the features of time- and tissue-specific expressions. CircRNAs have attracted increasing interest from scientists because of their non-negligible effects on the growth and development of organisms. The translation capability of circRNAs is a novel and valuable direction in the functional research of circRNAs. To explore the translation potential of circRNAs, some progress has been made in both experimental identification and computational prediction. For computational prediction, both CircCode and CircPro are ribosome profiling-based software applications for predicting translatable circRNAs, and the online databases riboCIRC and TransCirc analyze as many pieces of evidence as possible and list the predicted translatable circRNAs of high confidence. Simultaneously, mass spectrometry in proteomics is often recognized as an efficient method to support the identification of protein and peptide sequences from diverse complex templates. However, few applications fully utilize mass spectrometry to predict translatable circRNAs. Therefore, this research aims to build up a scientific analysis pipeline with two salient features: 1) it starts with the data analysis of raw tandem mass spectrometry data; and 2) it also incorporates other translation evidence such as IRES. The pipeline has been packaged into an analysis tool called mass spectrometry to translatable circRNAs (MStoCIRC). MStoCIRC is mainly implemented by Python3 language programming and could be downloaded from GitHub (https://github.com/QUMU00/mstocirc-master). The tool contains a main program and several small, independent function modules, making it more multifunctional. MStoCIRC can process data efficiently and has obtained hundreds of translatable circRNAs in humans and Arabidopsis thaliana.
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14
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Dal Molin A, Gaffo E, Difilippo V, Buratin A, Tretti Parenzan C, Bresolin S, Bortoluzzi S. CRAFT: a bioinformatics software for custom prediction of circular RNA functions. Brief Bioinform 2022; 23:6518047. [PMID: 35106564 PMCID: PMC8921651 DOI: 10.1093/bib/bbab601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/10/2021] [Accepted: 12/26/2021] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs), transcripts generated by backsplicing, are particularly stable and pleiotropic molecules, whose dysregulation drives human diseases and cancer by modulating gene expression and signaling pathways. CircRNAs can regulate cellular processes by different mechanisms, including interaction with microRNAs (miRNAs) and RNA-binding proteins (RBP), and encoding specific peptides. The prediction of circRNA functions is instrumental to interpret their impact in diseases, and to prioritize circRNAs for functional investigation. Currently, circRNA functional predictions are provided by web databases that do not allow custom analyses, while self-standing circRNA prediction tools are mostly limited to predict only one type of function, mainly focusing on the miRNA sponge activity of circRNAs. To solve these issues, we developed CRAFT (CircRNA Function prediction Tool), a freely available computational pipeline that predicts circRNA sequence and molecular interactions with miRNAs and RBP, along with their coding potential. Analysis of a set of circRNAs with known functions has been used to appraise CRAFT predictions and to optimize its setting. CRAFT provides a comprehensive graphical visualization of the results, links to several knowledge databases, and extensive functional enrichment analysis. Moreover, it originally combines the predictions for different circRNAs. CRAFT is a useful tool to help the user explore the potential regulatory networks involving the circRNAs of interest and generate hypotheses about the cooperation of circRNAs into the modulation of biological processes.
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Affiliation(s)
- Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy.,Department of Biology, University of Padova, Padova, Italy
| | - Caterina Tretti Parenzan
- Onco-hematology, stem cell transplant and gene therapy laboratory, IRP-Istituto di Ricerca Pediatrica, Padova, Italy.,Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University Hospital
| | - Silvia Bresolin
- Onco-hematology, stem cell transplant and gene therapy laboratory, IRP-Istituto di Ricerca Pediatrica, Padova, Italy.,Pediatric Hematology, Oncology and Stem Cell Transplant Division, Women and Child Health Department, Padua University Hospital
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy.,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, Padova, Italy
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15
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Oliveira LS, Patera AC, Domingues DS, Sanches DS, Lopes FM, Bugatti PH, Saito PTM, Maracaja-Coutinho V, Durham AM, Paschoal AR. Computational Analysis of Transposable Elements and CircRNAs in Plants. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2362:147-172. [PMID: 34195962 DOI: 10.1007/978-1-0716-1645-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter provides two main contributions: (1) a description of computational tools and databases used to identify and analyze transposable elements (TEs) and circRNAs in plants; and (2) data analysis on public TE and circRNA data. Our goal is to highlight the primary information available in the literature on circular noncoding RNAs and transposable elements in plants. The exploratory analysis performed on publicly available circRNA and TEs data help discuss four sequence features. Finally, we investigate the association on circRNAs:TE in plants in the model organism Arabidopsis thaliana.
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Affiliation(s)
- Liliane Santana Oliveira
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil. .,Embrapa Soja, Londrina, Paraná, Brazil.
| | - Andressa Caroline Patera
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Douglas Silva Domingues
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil.,Group of Genomics and Transcriptomes in Plants, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Danilo Sipoli Sanches
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Fabricio Martins Lopes
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Pedro Henrique Bugatti
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Priscila Tiemi Maeda Saito
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Vinicius Maracaja-Coutinho
- Centro de Modelamiento Molecular, Biofísica y Bioinformática-CM2B2, Facultad de Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago, Chile
| | - Alan Mitchell Durham
- Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), Cidade Universitária, SP, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil.
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16
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Zhao X, Zhong Y, Wang X, Shen J, An W. Advances in Circular RNA and Its Applications. Int J Med Sci 2022; 19:975-985. [PMID: 35813288 PMCID: PMC9254372 DOI: 10.7150/ijms.71840] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/15/2022] [Indexed: 11/17/2022] Open
Abstract
Circular RNA (circRNA) is a novel endogenous non-coding RNA (ncRNA) that, like microRNA (miRNA), is a rapidly emerging RNA research topic. CircRNA, unlike traditional linear RNAs (which have 5' and 3' ends), has a closed-loop structure that is unaffected by RNA exonucleases. Thus, circRNA has sustained expression and is less sensitive to degradation. Since circRNAs have many miRNAs binding sites, eliminating their repressive effects on their target genes can strongly enhance their expression. CircRNAs serve an important regulatory role in disease onset and progression via specific circRNA-miRNA interactions. We summarized the current progress in elucidating mechanisms and biogenesis of circRNAs in this review. In particular, circRNAs can function mainly as miRNA sponges, regulating host gene expression and protein transportation. Finally, we discussed the application prospects and significant challenges for the development of circRNA-based therapeutics.
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Affiliation(s)
- Xian Zhao
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Youxiu Zhong
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Xudong Wang
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Jiuheng Shen
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
| | - Wenlin An
- National Vaccine & Serum Institute (NVSI), China National Biotech Group (CNBG), No. 38 Jing Hai Second Road, Beijing, 101111, China
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17
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Chioccarelli T, Falco G, Cappetta D, De Angelis A, Roberto L, Addeo M, Ragusa M, Barbagallo D, Berrino L, Purrello M, Ambrosino C, Cobellis G, Pierantoni R, Chianese R, Manfrevola F. FUS driven circCNOT6L biogenesis in mouse and human spermatozoa supports zygote development. Cell Mol Life Sci 2021; 79:50. [PMID: 34936029 PMCID: PMC8739325 DOI: 10.1007/s00018-021-04054-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/10/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023]
Abstract
Circular RNA (circRNA) biogenesis requires a backsplicing reaction, promoted by inverted repeats in cis-flanking sequences and trans factors, such as RNA-binding proteins (RBPs). Among these, FUS plays a key role. During spermatogenesis and sperm maturation along the epididymis such a molecular mechanism has been poorly explored. With this in mind, we chose circCNOT6L as a study case and wild-type (WT) as well as cannabinoid receptor type-1 knock-out (Cb1−/−) male mice as animal models to analyze backsplicing mechanisms. Our results suggest that spermatozoa (SPZ) have an endogenous skill to circularize mRNAs, choosing FUS as modulator of backsplicing and under CB1 stimulation. A physical interaction between FUS and CNOT6L as well as a cooperation among FUS, RNA Polymerase II (RNApol2) and Quaking (QKI) take place in SPZ. Finally, to gain insight into FUS involvement in circCNOT6L biogenesis, FUS expression was reduced through RNA interference approach. Paternal transmission of FUS and CNOT6L to oocytes during fertilization was then assessed by using murine unfertilized oocytes (NF), one-cell zygotes (F) and murine oocytes undergoing parthenogenetic activation (PA) to exclude a maternal contribution. The role of circCNOT6L as an active regulator of zygote transition toward the 2-cell-like state was suggested using the Embryonic Stem Cell (ESC) system. Intriguingly, human SPZ exactly mirror murine SPZ.
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Affiliation(s)
- Teresa Chioccarelli
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
| | - Geppino Falco
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy.,Istituto di Ricerche Genetiche Gaetano Salvatore, Biogem scarl, Ariano Irpino, Avellino, Italy
| | - Donato Cappetta
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
| | - Antonella De Angelis
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
| | - Luca Roberto
- Istituto di Ricerche Genetiche Gaetano Salvatore, Biogem scarl, Ariano Irpino, Avellino, Italy
| | - Martina Addeo
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Marco Ragusa
- Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Davide Barbagallo
- Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Liberato Berrino
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
| | - Michele Purrello
- Dipartimento di Scienze Biomediche e Biotecnologiche, Università di Catania, Via Santa Sofia 97, 95123, Catania, Italy
| | - Concetta Ambrosino
- Istituto di Ricerche Genetiche Gaetano Salvatore, Biogem scarl, Ariano Irpino, Avellino, Italy.,Dipartimento di Scienze e Tecnologie, Università del Sannio, Benevento, Italy
| | - Gilda Cobellis
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
| | - Riccardo Pierantoni
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
| | - Rosanna Chianese
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy.
| | - Francesco Manfrevola
- Dipartimento di Medicina Sperimentale, Sez. Bottazzi, Università degli Studi della Campania "L. Vanvitelli", Via Costantinopoli 16, 80138, Napoli, Italy
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18
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Cai Zhang, Li B, Huang Y, Gao S, Gao X. Biogenesis, Functions, and Cancer Relationships of a Specific Circular RNA: CircFoxo3. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s106816202106025x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Sharma D, Sehgal P, Sivasubbu S, Scaria V. A genome-wide circular RNA transcriptome in rat. Biol Methods Protoc 2021; 6:bpab016. [PMID: 34527809 PMCID: PMC8435660 DOI: 10.1093/biomethods/bpab016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that back-splice from 5ʹ donor site and 3ʹ acceptor sites to form a circular structure. A number of circRNAs have been discovered in model organisms including human, mouse, Drosophila, among other organisms. There are a few candidate-based studies on circRNAs in rat, a well-studied model organism as well. A number of pipelines have been published to identify the back splice junctions for the discovery of circRNAs but studies comparing these tools have suggested that a combination of tools would be a better approach to identify high-confidence circRNAs. The availability of a recent dataset of transcriptomes encompassing 11 tissues, 4 developmental stages, and 2 genders motivated us to explore the landscape of circRNAs in the organism in this context. In order to understand the difference among different pipelines, we employed five different combinations of tools to identify circular RNAs from the dataset. We compared the results of the different combination of tools/pipelines with respect to alignment, total number of circRNAs identified and read-coverage. In addition, we identified tissue-specific, development-stage specific and gender-specific circRNAs and further independently validated 16 circRNA junctions out of 24 selected candidates in 5 tissue samples and estimated the quantitative expression of five circRNA candidates using real-time polymerase chain reaction and our analysis suggests three candidates as tissue-enriched. This study is one of the most comprehensive studies which provides a map of circRNAs transcriptome as well as to understand the difference among different computational pipelines in rat.
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Affiliation(s)
- Disha Sharma
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Paras Sehgal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road (CSIR-IGIB), Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road (CSIR-IGIB), Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
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20
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Gaffo E, Buratin A, Dal Molin A, Bortoluzzi S. Bioinformatic Analysis of Circular RNA Expression. Methods Mol Biol 2021; 2348:343-370. [PMID: 34160817 DOI: 10.1007/978-1-0716-1581-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Circular RNAs (circRNAs) are stable RNA molecules generated by backsplicing that play regulatory functions through interaction with other RNA and proteins, as well as by encoding peptides. Dysregulation of circRNA expression can drive cancer development and progression with different mechanisms. CircRNAs are currently regarded as extremely attractive molecules in cancer research for the identification of new and possibly targetable disease regulatory networks and for the development of biomarkers for cancer diagnosis, prognosis definition, and monitoring. Using specific experimental and computational protocols, circRNAs can be identified through RNA-seq by spotting the reads spanning backsplice junctions, which are specific to circular molecules. In this chapter, we report a state-of-the-art computational protocol for a genome-wide analysis of circRNAs from RNA-seq data, which considers circRNA detection, quantification, and differential expression testing. Finally, we indicate how to determine circular transcript sequences and the resources for an in silico functional characterization of circRNAs.
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Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy.,Department of Biology, University of Padova, Padova, Italy
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy. .,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, Padova, Italy.
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21
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Advances in Computational Methodologies for Classification and Sub-Cellular Locality Prediction of Non-Coding RNAs. Int J Mol Sci 2021; 22:8719. [PMID: 34445436 PMCID: PMC8395733 DOI: 10.3390/ijms22168719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
Apart from protein-coding Ribonucleic acids (RNAs), there exists a variety of non-coding RNAs (ncRNAs) which regulate complex cellular and molecular processes. High-throughput sequencing technologies and bioinformatics approaches have largely promoted the exploration of ncRNAs which revealed their crucial roles in gene regulation, miRNA binding, protein interactions, and splicing. Furthermore, ncRNAs are involved in the development of complicated diseases like cancer. Categorization of ncRNAs is essential to understand the mechanisms of diseases and to develop effective treatments. Sub-cellular localization information of ncRNAs demystifies diverse functionalities of ncRNAs. To date, several computational methodologies have been proposed to precisely identify the class as well as sub-cellular localization patterns of RNAs). This paper discusses different types of ncRNAs, reviews computational approaches proposed in the last 10 years to distinguish coding-RNA from ncRNA, to identify sub-types of ncRNAs such as piwi-associated RNA, micro RNA, long ncRNA, and circular RNA, and to determine sub-cellular localization of distinct ncRNAs and RNAs. Furthermore, it summarizes diverse ncRNA classification and sub-cellular localization determination datasets along with benchmark performance to aid the development and evaluation of novel computational methodologies. It identifies research gaps, heterogeneity, and challenges in the development of computational approaches for RNA sequence analysis. We consider that our expert analysis will assist Artificial Intelligence researchers with knowing state-of-the-art performance, model selection for various tasks on one platform, dominantly used sequence descriptors, neural architectures, and interpreting inter-species and intra-species performance deviation.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- National Center for Artificial Intelligence (NCAI), National University of Sciences and Technology, Islamabad 44000, Pakistan;
- School of Electrical Engineering & Computer Science, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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22
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Sinha T, Panigrahi C, Das D, Chandra Panda A. Circular RNA translation, a path to hidden proteome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1685. [PMID: 34342387 DOI: 10.1002/wrna.1685] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/06/2022]
Abstract
Functional proteins in the cell are translated from the messenger RNA (mRNA) molecules, constituting less than 5% of the cellular transcriptome. The majority of the RNA molecules in the cell are noncoding RNAs, including rRNA, tRNA, snRNA, piRNA, lncRNA, microRNA, and poorly characterized circular RNAs (circRNAs). Recent studies established that circRNAs regulate gene expression by associating with RNA-binding proteins and microRNAs. With the growing understanding of circRNA functions, a subset of circRNAs has been reported to translate into proteins. Interestingly, the presence of Open Reading Frames (ORFs), N6-methyladenosine (m6A) modifications, and internal ribosomal entry sites (IRES) in the circRNA sequences indicate their coding potential through the cap-independent translation initiation mechanism. The purpose of this review is to highlight the mechanism of circRNA translation and the importance of circRNA-encoded proteins (circ-proteins) in cellular physiology and pathology. Here, we discuss the computational and molecular methods currently utilized to systematically identify translatable circRNAs and the functional characterization of the circ-proteins. We foresee that the ongoing and future studies on circRNA translation will uncover the hidden proteome and their therapeutic implications in human health. This article is categorized under: RNA Methods > RNA Analyses in Cells Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Translation > Mechanisms.
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Affiliation(s)
- Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Chirag Panigrahi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Debojyoti Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India.,School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
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23
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Function of Circular RNAs in Fish and Their Potential Application as Biomarkers. Int J Mol Sci 2021; 22:ijms22137119. [PMID: 34281172 PMCID: PMC8268770 DOI: 10.3390/ijms22137119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.
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24
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Ferrero G, Licheri N, De Bortoli M, Calogero RA, Beccuti M, Cordero F. Computational Analysis of circRNA Expression Data. Methods Mol Biol 2021; 2284:181-192. [PMID: 33835443 DOI: 10.1007/978-1-0716-1307-8_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Analysis of circular RNA (circRNA) expression from RNA-Seq data can be performed with different algorithms and analysis pipelines, tools allowing the extraction of heterogeneous information on the expression of this novel class of RNAs. Computational pipelines were developed to facilitate the analysis of circRNA expression by leveraging different public tools in easy-to-use pipelines. This chapter describes the complete workflow for a computationally reproducible analysis of circRNA expression starting for a public RNA-Seq experiment. The main steps of circRNA prediction, annotation, classification, sequence reconstruction, quantification, and differential expression are illustrated.
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Affiliation(s)
- Giulio Ferrero
- Department of Computer Science, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Nicola Licheri
- Department of Computer Science, University of Turin, Turin, Italy
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Marco Beccuti
- Department of Computer Science, University of Turin, Turin, Italy
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25
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Yesharim L, Mojbafan M, Abiri M. Hints From the Cellular Functions to the Practical Outlook of Circular RNAs. Front Genet 2021; 12:679446. [PMID: 34220952 PMCID: PMC8247595 DOI: 10.3389/fgene.2021.679446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/25/2021] [Indexed: 12/29/2022] Open
Abstract
Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian cells, these subtypes of RNAs’ capabilities have come into focus in recent years. The unique structure and various functional roles of circRNAs in many cellular processes have aroused researchers’ interest and raised many questions about whether circRNAs can facilitate the diagnosis and treatment of diseases. To answer these questions, we will illustrate the main known functions and regulatory roles of circRNAs in the cell after presenting a brief history of the discovery of circRNAs and the main proposed theories of the biogenesis of circRNAs. Afterward, the practical application of circRNAs as biomarkers of different pathophysiological conditions will be discussed, mentioning some examples and challenges in this area. We also consider one of the main questions that human beings have always been faced, “the origin of life,” and its possible connection to circRNAs. Finally, focusing on the various capabilities of circRNAs, we discuss their potential therapeutic applications considering the immunity response toward exogenous circRNAs. However, there are still disputes about the exact immune system reaction, which we will discuss in detail.
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Affiliation(s)
- Liora Yesharim
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Mojbafan
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, Ali-Asghar Children's Hospital, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Shahid Akbarabadi Clinical Research Development Unit (ShACRDU), Iran University of Medical Sciences, Tehran, Iran
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26
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Lu Y, Li Z, Lin C, Zhang J, Shen Z. Translation role of circRNAs in cancers. J Clin Lab Anal 2021; 35:e23866. [PMID: 34097315 PMCID: PMC8275004 DOI: 10.1002/jcla.23866] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) constitute a class of covalently closed RNA molecules. With the continuous advancement of high‐throughput sequencing technology and bioinformatics tools, many circRNAs have been identified in various human tissues and cell lines. Notably, recent studies have indicated that some circRNAs have translational functions. Internal ribosome entry sites and the N6‐methyladenosine modification mediate cap‐independent translation. This review describes these two translation mechanisms and verification methods at the molecular level. Databases (including ORF Finder, Pfam, BLASTp, CircRNADb, CircBase, CircPro, CircCode, IRESite, IRESbase) were used to analyze whether circRNAs have the structural characteristic of translation. CircRNA minigene reporter system containing green fluorescent protein (GFP) confirmed the translation potential of circRNAs. Also, we briefly summarize the roles of proteins/peptides encoded by circRNAs (circFBXW7, circFNDC3B, circLgr4, circPPP1R12A, circMAPK1, circβ‐catenin, circGprc5a, circ‐SHPRH, circPINTexon2, circAKT3) that have been verified thus far in human cancers (triple‐negative breast cancer, colon cancer, gastric cancer, hepatocellular carcinoma, bladder cancer, glioblastoma). Those findings suggest circRNAs have a great implication in translation of the human genome.
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Affiliation(s)
- Yaqin Lu
- Ningbo University School of MedicineNingboChina
| | - Zhe Li
- Ningbo University School of MedicineNingboChina
| | - Chen Lin
- Ningbo University School of MedicineNingboChina
| | - Jian Zhang
- Li Huili Hospital Affiliated to Ningbo University SchoolNingboChina
| | - Zhisen Shen
- Li Huili Hospital Affiliated to Ningbo University SchoolNingboChina
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27
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Ward Z, Pearson J, Schmeier S, Cameron V, Pilbrow A. Insights into circular RNAs: their biogenesis, detection, and emerging role in cardiovascular disease. RNA Biol 2021; 18:2055-2072. [PMID: 33779499 DOI: 10.1080/15476286.2021.1891393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Circular RNAs (circRNAs) are an evolutionarily conserved form of noncoding RNA with covalently closed loop structures. Initial studies established a functional role for circRNAs as potent microRNA sponges and many other studies have focussed solely on this. However, the biological functions of most circRNAs are still undetermined and other functional roles are gaining traction. These include protein sponges and regulators, and coding for proteins with an alternative mechanism of translation, potentially opening up a whole new transcriptome. The first step to gaining insight into circRNA function is accurate identification and various software platforms have been developed. Specialized detection software has now evolved into whole bioinformatics pipelines that can be used for detection, de novo identification, functional prediction, and validation of circRNAs. However, few cardiovascular circRNA studies have utilized these tools. This review summarizes current knowledge of circRNA biogenesis, bioinformatic detection tools and the emerging role of circRNAs in cardiovascular disease.
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Affiliation(s)
- Zoe Ward
- Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Sebastian Schmeier
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Vicky Cameron
- Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
| | - Anna Pilbrow
- Christchurch Heart Institute, University of Otago, Christchurch, New Zealand
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28
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Wang X, Li H, Lu Y, Cheng L. Circular RNAs in Human Cancer. Front Oncol 2021; 10:577118. [PMID: 33537235 PMCID: PMC7848167 DOI: 10.3389/fonc.2020.577118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 12/02/2020] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous single-stranded covalently closed RNAs, primarily produced from pre-mRNAs via non-canonical back-splicing. circRNAs are highly conserved, stable, and expressed in tissue- and development-specific pattern. circRNAs play essential roles in physiological process as well as cancer biology. By the advances of deep sequencing and bioinformatics, the number of circRNAs have increased explosively. circRNAs function as miRNA/protein sponge, protein scaffold, protein recruitment, enhancer of protein function, as well as templates for translation involved in the regulation of transcription/splicing, translation, protein degradation, and pri-miRNA processing in human cancers and contributed to the pathogenesis of cancer. Numerous circRNAs may function in diverse manners. In this review, we survey the current understanding of circRNA functions in human cancer including miRNA sponge, circRNA-protein interaction, and circRNA-encoded protein, and summarize available databases for circRNA annotation and functional prediction.
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Affiliation(s)
- Xiong Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Huijun Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
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29
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Zhang J, Liu R, Li G. Constructing CircRNA-miRNA-mRNA Regulatory Networks by Using GreenCircRNA Database. Methods Mol Biol 2021; 2362:173-179. [PMID: 34195963 DOI: 10.1007/978-1-0716-1645-1_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Circular RNA (circRNA) is a special class of endogenous RNA with a continuous loop structure, which plays important roles in metabolic processes. With the development of sequencing technology and algorithm for circRNA, more and more circRNA are identified in plants. However, the function of most plant circRNA remains unclear. In order to investigate the function of plant circRNA, we firstly build a plant circRNA database, named GreenCircRNA. Then we construct circRNA-miRNA-mRNA regulatory networks to infer the function of plant circRNA. Here, taking Arabidopsis thaliana as an example, we firstly show the method for identification of circRNA and construction of circRNA-miRNA-mRNA networks based on GreenCircRNA database, then perform a case study for identifying circRNAs and inferring their function in A. thaliana. Our method can be easily extended and applied to other plants.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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30
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Huang Y, Wang Y, Zhang C, Sun X. Biological functions of circRNAs and their progress in livestock and poultry. Reprod Domest Anim 2020; 55:1667-1677. [DOI: 10.1111/rda.13816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Yong Huang
- College of Animal Science and Technology Henan University of Science and Technology Luoyang China
| | - Yanli Wang
- Development Planning Office Henan University of Science and Technology Luoyang China
| | - Cai Zhang
- College of Animal Science and Technology Henan University of Science and Technology Luoyang China
| | - Xihong Sun
- Development Planning Office Henan University of Science and Technology Luoyang China
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31
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Zhou B, Yang H, Yang C, Bao YL, Yang SM, Liu J, Xiao YF. Translation of noncoding RNAs and cancer. Cancer Lett 2020; 497:89-99. [PMID: 33038492 DOI: 10.1016/j.canlet.2020.10.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
The human genome contains thousands of noncoding RNAs (ncRNAs), which are thought to lack open reading frames (ORFs) and cannot be translated. Some ncRNAs reportedly have important functions, including epigenetic regulation, chromatin remolding, protein modification, and RNA degradation, but the functions of most ncRNAs remain elusive. Through the application and development of ribosome profiling and sequencing technologies, an increasing number of studies have discovered the translation of ncRNAs. Although ncRNAs were initially defined as noncoding RNAs, a number of ncRNAs actually contain ORFs that are translated into peptides. Here, we summarize the available methods, tools, and databases for identifying and validating ncRNA-encoded peptides/proteins, and the recent findings regarding ncRNA-encoded small peptides/proteins in cancer are compiled and synthesized. Importantly, the role of ncRNA-encoding peptides/proteins has application prospects in cancer research, but some potential challenges remain unresolved. The aim of this review is to provide a theoretical basis that might promote the discovery of more peptides/proteins encoded by ncRNAs and aid the further development of novel diagnostic and prognostic cancer markers and therapeutic targets.
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Affiliation(s)
- Bo Zhou
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Huan Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Chuan Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Yu-Lu Bao
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China
| | - Jiao Liu
- Department of Endoscope, General Hospital of Northern Theater Command, Shenyang, 110016, Liaoning, China.
| | - Yu-Feng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Chongqing, 400037, China.
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32
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Fu X, Yang Y, Shen YQ, Zhou XG, Zhou XY. [Continuous expression and functional prediction of circular RNA in mouse lung development]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1125-1130. [PMID: 33059812 PMCID: PMC7568991 DOI: 10.7499/j.issn.1008-8830.2004071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To study the continuous expression and potential function of circular RNA (circRNA), circ4:150439343|150477468 and circ15:73330849|73343359, in mouse lung development. METHODS According to the stage of lung development, lung tissue samples were collected from mice on embryonic day 16.5 (E16.5), embryonic day 18.5 (E18.5), and postnatal day 2 (P2). Hematoxylin and eosin staining was performed to observe the morphology of lung tissue. Quantitative real-time PCR (qRT-PCR) was used to measure the mRNA expression of circ4:150439343|150477468 and circ15:73330849|73343359 during late lung development; miRanda and TargetScan were used to predict the target miRNAs of circRNAs, and then GO and KEGG analysis was performed for the target genes to predict the potential function of circRNAs. RESULTS Type II alveolar epithelial cells were observed in the lung slices of E16.5 mice, with a gradual increase in number. On P2, the pulmonary alveoli expanded rapidly, the pulmonary interstitium became thinner, and the alveolar structure gradually became mature. The results of qRT-PCR showed that the relative expression of circ4:150439343|150477468 was continuously upregulated over time and the relative expression of circ15:73330849|73343359 was first downregulated and then upregulated (P<0.05). The KEGG and GO analysis showed that circRNAs were involved in the Notch, PI3K-Akt, and NF-κB signaling pathways. CONCLUSIONS Circ4:150439343|150477468 and circ15:73330849|73343359 can participate in lung development through the Notch signaling pathway.
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Affiliation(s)
- Xue Fu
- Neonatal Medical Center, Children's Hospital Affiliated to Nanjing Medical University, Nanjing 210008, China.
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33
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Fan C, Lei X, Pan Y. Prioritizing CircRNA-Disease Associations With Convolutional Neural Network Based on Multiple Similarity Feature Fusion. Front Genet 2020; 11:540751. [PMID: 33193615 PMCID: PMC7525185 DOI: 10.3389/fgene.2020.540751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022] Open
Abstract
Accumulating evidence shows that circular RNAs (circRNAs) have significant roles in human health and in the occurrence and development of diseases. Biological researchers have identified disease-related circRNAs that could be considered as potential biomarkers for clinical diagnosis, prognosis, and treatment. However, identification of circRNA–disease associations using traditional biological experiments is still expensive and time-consuming. In this study, we propose a novel method named MSFCNN for the task of circRNA–disease association prediction, involving two-layer convolutional neural networks on a feature matrix that fuses multiple similarity kernels and interaction features among circRNAs, miRNAs, and diseases. First, four circRNA similarity kernels and seven disease similarity kernels are constructed based on the biological or topological properties of circRNAs and diseases. Subsequently, the similarity kernel fusion method is used to integrate the similarity kernels into one circRNA similarity kernel and one disease similarity kernel, respectively. Then, a feature matrix for each circRNA–disease pair is constructed by integrating the fused circRNA similarity kernel and fused disease similarity kernel with interactions and features among circRNAs, miRNAs, and diseases. The features of circRNA–miRNA and disease–miRNA interactions are selected using principal component analysis. Finally, taking the constructed feature matrix as an input, we used two-layer convolutional neural networks to predict circRNA–disease association labels and mine potential novel associations. Five-fold cross validation shows that our proposed model outperforms conventional machine learning methods, including support vector machine, random forest, and multilayer perception approaches. Furthermore, case studies of predicted circRNAs for specific diseases and the top predicted circRNA–disease associations are analyzed. The results show that the MSFCNN model could be an effective tool for mining potential circRNA–disease associations.
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Affiliation(s)
- Chunyan Fan
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yi Pan
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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34
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Disease-Associated Circular RNAs: From Biology to Computational Identification. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6798590. [PMID: 32908906 PMCID: PMC7450300 DOI: 10.1155/2020/6798590] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.
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35
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Artemaki PI, Scorilas A, Kontos CK. Circular RNAs: A New Piece in the Colorectal Cancer Puzzle. Cancers (Basel) 2020; 12:cancers12092464. [PMID: 32878117 PMCID: PMC7564116 DOI: 10.3390/cancers12092464] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third most fatal type of malignancy, worldwide. Despite the advances accomplished in the elucidation of its molecular base and the existing CRC biomarkers introduced in the clinical practice, additional research is required. Circular RNAs (circRNAs) constitute a new RNA type, formed by back-splicing of primary transcripts. They have been discovered during the 1970s but were characterized as by-products of aberrant splicing. However, the modern high-throughput approaches uncovered their widespread expression; therefore, several questions were raised regarding their potential biological roles. During the last years, great progress has been achieved in the elucidation of their functions: circRNAs can act as microRNA sponges, transcription regulators, and interfere with splicing, as well. Furthermore, they are heavily involved in various human pathological states, including cancer, and could serve as diagnostic and prognostic biomarkers in several diseases. Particularly in CRC, aberrant expression of circRNAs has been observed. More specifically, these molecules either inhibit or promote colorectal carcinogenesis by regulating different molecules and signaling pathways. The present review discusses the characteristics and functions of circRNA, prior to analyzing the multifaceted role of these molecules in CRC and their potential value as biomarkers and therapeutic targets.
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Affiliation(s)
- Pinelopi I Artemaki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, GR-15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, GR-15701 Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, GR-15701 Athens, Greece
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36
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Zhang JR, Sun HJ. Roles of circular RNAs in diabetic complications: From molecular mechanisms to therapeutic potential. Gene 2020; 763:145066. [PMID: 32827686 DOI: 10.1016/j.gene.2020.145066] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023]
Abstract
Diabetes is characterized by changed homeostasis of blood glucose levels, which is associated with various complications, including cardiomyopathy, atherosclerosis, endothelial dysfunction, nephropathy, retinopathy and neuropathy. In recent years, accumulative evidence has demonstrated that circular RNAs are identified as a novel type of noncoding RNAs (ncRNAs) involving in the regulation of various physiological processes and pathologic conditions. Specifically, the emergence of complications response to diabetes is finely controlled by a complex gene regulatory network in which circular RNAs play a critical role. Recently, circular RNAs are emerging as messengers that could influence cellular functions under diabetic conditions. Dysregulation of circular RNAs has been closely linked to the pathophysiology of diabetes-related complications. In this review, we aimed to summarize the current progression and underlying mechanisms of circular RNA in the development of diabetes-related complications. We will also provide an overview of circular RNA-regulated cell communications in different types of cells that have been linked to diabetic complications. We anticipated that the completion of this review will provide potential clues for developing novel circular RNAs-based biomarkers or therapeutic targets for diabetes and its associated complications.
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Affiliation(s)
- Ji-Ru Zhang
- Department of Anesthesiology, Affiliated Hospital of Jiangnan University, Wuxi 214062, PR China
| | - Hai-Jian Sun
- Department of Basic Medicine, Wuxi Medical School, Jiangnan University, Wuxi 214122, PR China; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
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37
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Sun P, Wang H, Li G. Rcirc: An R Package for circRNA Analyses and Visualization. Front Genet 2020; 11:548. [PMID: 32582287 PMCID: PMC7290040 DOI: 10.3389/fgene.2020.00548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/07/2020] [Indexed: 11/16/2022] Open
Abstract
Circular RNA (circRNA), which has a closed-loop structure, is a special type of endogenous RNA that plays important roles in many biological processes. With improvements in next-generation sequencing technology and bioinformatics methods, some tools have been published for circRNA detection based on RNA-seq. Here, we developed the R package “Rcirc” for further analyses of circRNA after its detection. Rcirc identifies the coding ability of circRNA and visualizes various aspects of this feature. It also provides general visualization for both single circRNAs and meta-features of thousands of circRNAs. Rcirc was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on GitHub (https://github.com/PSSUN/Rcirc) under the license GPL 3.0.
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Affiliation(s)
- Peisen Sun
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.,College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haoming Wang
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.,College of Life Sciences, Shaanxi Normal University, Xi'an, China
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38
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Shi Y, Jia X, Xu J. The new function of circRNA: translation. Clin Transl Oncol 2020; 22:2162-2169. [PMID: 32449127 DOI: 10.1007/s12094-020-02371-1] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/01/2020] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) have been considered a special class of non-coding RNAs without 5' caps and 3' tails which are covalently closed RNA molecules generated by back splicing of mRNA. For a long time, circRNAs have been considered to be directly involved in various biological processes as functional RNA. In recent years, a variety of circRNAs have been found to have translational functions, and the resultant peptides also play biological roles in the emergence and progression of human disease. The discovery of these circRNAs and their encoded peptides has enriched genomics, helped us to study the causes of diseases, and promoted the development of biotechnology. The purpose of this review is to summarize the research progress of the detection methods, translation initiation mechanism, as well as functional mechanism of peptides encoded by circRNAs, with the goal of providing the directions for the discovery of biomarkers for diagnosis, prognosis, and therapeutic targets for human disease.
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Affiliation(s)
- Y Shi
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, No.123, Tianfei Xiang, Mochou Road, Nanjing, 210004, China
| | - X Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, No.123, Tianfei Xiang, Mochou Road, Nanjing, 210004, China.
| | - J Xu
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, No.123, Tianfei Xiang, Mochou Road, Nanjing, 210004, China.
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Zaiou M. circRNAs Signature as Potential Diagnostic and Prognostic Biomarker for Diabetes Mellitus and Related Cardiovascular Complications. Cells 2020; 9:cells9030659. [PMID: 32182790 PMCID: PMC7140626 DOI: 10.3390/cells9030659] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) belong to the ever-growing class of naturally occurring noncoding RNAs (ncRNAs) molecules. Unlike linear RNA, circRNAs are covalently closed transcripts mostly generated from precursor-mRNA by a non-canonical event called back-splicing. They are highly stable, evolutionarily conserved, and widely distributed in eukaryotes. Some circRNAs are believed to fulfill a variety of functions inside the cell mainly by acting as microRNAs (miRNAs) or RNA-binding proteins (RBPs) sponges. Furthermore, mounting evidence suggests that the misregulation of circRNAs is among the first alterations in various metabolic disorders including obesity, hypertension, and cardiovascular diseases. More recent research has revealed that circRNAs also play a substantial role in the pathogenesis of diabetes mellitus (DM) and related vascular complications. These findings have added a new layer of complexity to our understanding of DM and underscored the need to reexamine the molecular pathways that lead to this disorder in the context of epigenetics and circRNA regulatory mechanisms. Here, I review current knowledge about circRNAs dysregulation in diabetes and describe their potential role as innovative biomarkers to predict diabetes-related cardiovascular (CV) events. Finally, I discuss some of the actual limitations to the promise of these RNA transcripts as emerging therapeutics and provide recommendations for future research on circRNA-based medicine.
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Affiliation(s)
- Mohamed Zaiou
- School of Pharmacy, Institut Jean-Lamour, The University of Lorraine, 7 Avenue de la Foret de Haye, CEDEX BP 90170, 54500 Vandoeuvre les Nancy, France
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40
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Lei M, Zheng G, Ning Q, Zheng J, Dong D. Translation and functional roles of circular RNAs in human cancer. Mol Cancer 2020; 19:30. [PMID: 32059672 PMCID: PMC7023758 DOI: 10.1186/s12943-020-1135-7] [Citation(s) in RCA: 400] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are a new class of non-coding RNAs formed by covalently closed loops through backsplicing. Recent methodologies have enabled in-depth characterization of circRNAs for identification and potential functions. CircRNAs play important roles in various biological functions as microRNA sponges, transcriptional regulators and combining with RNA binding proteins. Recent studies indicated that some cytoplasmic circRNAs can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cellular physiology function. Internal Ribosome Entry site (IRES)- and N6-methyladenosines (m6A)-mediated cap-independent translation initiation have been suggested to be potential mechanism for circRNA translation. To date, several translated circRNAs have been uncovered to play pivotal roles in human cancers. In this review, we introduced the properties and functions of circRNAs, and characterized the possible mechanism of translation initiation and complexity of the translation ability of circRNAs. We summarized the emerging functions of circRNA-encoded proteins in human cancer. The works on circRNA translation will open a hidden human proteome, and enhance us to understand the importance of circRNAs in human cancer, which has been poorly explored so far.
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Affiliation(s)
- Ming Lei
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Guantao Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Qianqian Ning
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
| | - Dong Dong
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
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41
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Zeng K, Wang S. Circular RNAs: The crucial regulatory molecules in colorectal cancer. Pathol Res Pract 2020; 216:152861. [PMID: 32061452 DOI: 10.1016/j.prp.2020.152861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide. Recent studies have shown that circular RNAs (circRNAs) play critical roles in the pathogenesis and progression of CRC. CircRNAs are a special class of endogenous non-coding RNAs (ncRNAs) that harbor covalently closed ring structure with high conservation and stability, which are expressed in a tissue- and developmental-stage-specific manner. A growing body of evidence suggests that circRNAs are abnormally expressed in CRC tissues, cell lines and plasma, and are closely linked with CRC clinical malignant features. CircRNAs participate in various biological processes of CRC cells, including cell proliferation, apoptosis, senescence, migration and invasion and so on, through acting as "microRNA (miRNA) sponges", binding to protein and even translating protein. In the present review, we systematically introduce the CRC-related circRNAs and their functional mechanisms, as well as the potential applications for CRC diagnosis and prognosis.
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Affiliation(s)
- Kaixuan Zeng
- School of Medicine, Southeast University, Nanjing, 210009, China; General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing, 210009, China; General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
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Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21030792. [PMID: 31991793 PMCID: PMC7037704 DOI: 10.3390/ijms21030792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/09/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022] Open
Abstract
Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3′–5′ ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.
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Inferring Candidate CircRNA-Disease Associations by Bi-random Walk Based on CircRNA Regulatory Similarity. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7354774 DOI: 10.1007/978-3-030-53956-6_44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Identification of associations between circular RNAs (circRNA) and diseases has become a hot topic, which is beneficial for researchers to understand the disease mechanism. However, traditional biological experiments are expensive and time-consuming. In this study, we proposed a novel method named BWHCDA, which applied bi-random walk algorithm on the heterogeneous network for predicting circRNA-disease associations. First, circRNA regulatory similarity is measured based on circRNA-miRNA interactions, and circRNA similarity is calculated by the average of circRNA regulatory similarity and Gaussian interaction profiles (GIP) kernel similarity for circRNAs. Similarly, disease similarity is the mean of disease semantic similarity and GIP kernel similarity for diseases. Then, the heterogeneous network is constructed by integrating circRNA network, disease network via circRNA-disease associations. Subsequently, the bi-random walk algorithm is implemented on the heterogeneous network to predict circRNA-disease associations. Finally, we utilize leave-one-out cross validation and 10-fold cross validation frameworks to evaluate the prediction performance of BWHCDA method and obtain AUC of 0.9334 and 0.8764 ± 0.0038, respectively. Moreover, the predicted hsa_circ_0000519-gastric cancer association is analyzed. Results show that BWHCDA could be an effective resource for clinical experimental guidance.
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