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Tibenda JJ, Wang N, Li N, Dang Y, Zhu Y, Wang X, Zhang Z, Zhao Q. Research progress of circular RNAs in myocardial ischemia. Life Sci 2024; 352:122809. [PMID: 38908786 DOI: 10.1016/j.lfs.2024.122809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/18/2024] [Accepted: 06/04/2024] [Indexed: 06/24/2024]
Abstract
Circular RNAs (circRNAs) are a type of single-stranded RNA that forms a covalently closed continuous loop. Its structure, stability, properties, and cell- and tissue-specificity have gained considerable recognition in the research and clinical sectors, as its role has been observed in different diseases, such as cardiovascular diseases, cancers, and central nervous system diseases, etc. Cardiovascular disease is still named as the number one cause of death globally, with myocardial ischemia (MI) accounting for 15 % of mortality annually. A number of circRNAs have been identified and are being studied for their ability to reduce MI by inhibiting the molecular mechanisms associated with myocardial ischemia reperfusion injury, such as inflammation, oxidative stress, autophagy, apoptosis, and so on. CircRNAs play a significant role as crucial regulatory elements at transcriptional levels, regulating different proteins, and at posttranscriptional levels, having interactions with RNA-binding proteins, ribosomal proteins, micro-RNAS, and long non-coding RNAS, making it possible to exert their effects through the circRNA-miRNA-mRNA axis. CircRNAs are a potential novel biomarker and therapeutic target for myocardial ischemia and cardiovascular diseases in general. The purpose of this review is to summarize the relationship, function, and mechanism observed between circRNAs and MI injury, as well as to provide directions for future research and clinical trials.
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Affiliation(s)
- Jonnea Japhet Tibenda
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Niuniu Wang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Nuan Li
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Yanning Dang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Yafei Zhu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Xiaobo Wang
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Zhengjun Zhang
- Department of Cardiology, General Hospital of Ningxia Medical University, Ningxia, China.
| | - Qipeng Zhao
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China.
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Wang Z, Han X, Su X, Yang X, Wang X, Yan J, Qian Q, Wang H. Analysis of key circRNA events in the AOP framework of TCS acting on zebrafish based on the data-driven. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116507. [PMID: 38838465 DOI: 10.1016/j.ecoenv.2024.116507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Triclosan (TCS) is a broad-spectrum antibiotic widely used in various personal care products. Research has found that exposure to TCS can cause toxic effects on organisms including neurotoxicity, cardiotoxicity, disorders of lipid metabolism, and abnormal vascular development, and the corresponding toxic mechanisms are gradually delving into the level of abnormal expression of miRNA regulating gene expression. Although the downstream mechanism of TCS targeting miRNA abnormal expression to induce toxicity is gradually improving, its upstream mechanism is still in a fog. Starting from the abnormal expression data of circRNA in zebrafish larvae induced by TCS, this study conducted a hierarchical analysis of the expression levels of all circRNAs, differential circRNAs, and trend circRNAs, and identified 29 key circRNA events regulating miRNA abnormal expression. In combination with GO and KEGG, the effects of TCS exposure were analyzed from the function and signaling pathway of the corresponding circRNA host gene. Furthermore, based on existing literature evidence about the biological toxicity induced by TCS targeting miRNA as data support, a competing endogenous RNAs (ceRNA) network characterizing the regulatory relationship between circRNA and miRNA was constructed and optimized. Finally, a comprehensive Adverse Outcome Pathway (AOP) framework of multiple levels of events including circRNA, miRNA, mRNA, pathway, and toxicity endpoints was established to systematically elucidate the toxic mechanism of TCS. Moreover, the rationality of the AOP framework was verified from the expression level of miRNA and adverse outcomes such as neurotoxicity, cardiotoxicity, oxidative stress, and inflammatory response by knockdown of circRNA48. This paper not only provides the key circRNA events for exploring the upstream mechanism of miRNA regulating gene expression but also provides an AOP framework for comprehensively demonstrating the toxicity mechanism of TCS on zebrafish, which is a theoretical basis for subsequent hazard assessment and prevention and control of TCS.
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Affiliation(s)
- Zejun Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xiaowen Han
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xincong Su
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xiao Yang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Xuedong Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jin Yan
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Qiuhui Qian
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Huili Wang
- National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
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Yan J, Wang X, Fan Z, Xu Y, Zhang Y, Liu Y, Guo L, Liu D. Circ_0098823 binding with IGF2BP3 regulates DNM1L stability to promote metastasis of hepatocellular carcinoma via mitochondrial fission. Apoptosis 2024; 29:709-725. [PMID: 38459420 DOI: 10.1007/s10495-023-01903-8] [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] [Accepted: 10/15/2023] [Indexed: 03/10/2024]
Abstract
Hepatocellular carcinoma (HCC) is highly metastatic and invasive. CircRNA participates in gene regulation of multiple tumor metastases, but little is known whether it is a bystander or an actual player in HCC metastasis. We aim to explore the molecular mechanisms of novel circRNAs in HCC metastasis. RT-qPCR was used to detect the expression of 13 circRNAs derived by the ERBB3 gene. The function of circ_0098823 and DNM1L in HCC cells were estimated by CCK-8, transwell assays, flow cytometry, electron microscope, and in vivo experiments. RNA binding protein of circ_0098823 was confirmed by RNA pull-down, mass spectrometry, and RNA immunoprecipitation. The expression of DNM1L after IGF2BP3 knockdown was detected by RT-qPCR and western blot. Circ_0098823 was significantly up-regulated both in HCC tissues and HGF induced cell lines. Circ_0098823 overexpression significantly enhanced proliferation, migration, and invasion but decreased apoptosis of HCC cells, particularly promoted mitochondrial fission. Compared with the control group, the tumors in the circ_0098823 knockdown mice were significantly smaller and lighter. Circ_0098823 silencing suppressed DNM1L expression, a key molecule for fission, which enhanced proliferation, migration and invasion, and inhibited apoptosis of HCC cell. IGF2BP3 was a binding protein of circ_0098823. The expression and mRNA stability of DNM1L were down-regulated by IGF2BP3 knockdown. IGF2BP3 knockdown significantly alleviated the excessive migration, invasion and apoptosis of HCC cells caused by circ_0098823 overexpression. This study uncovered a novel circ_0098823 with tumor-promoting effect, and the mechanism by which circ_0098823 participates in HCC progression through IGF2BP3-guided DNM1L. Our study broadens molecular understanding of HCC progression.
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Affiliation(s)
- Jiuliang Yan
- Department of Pancreatic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xiaofeng Wang
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zongyu Fan
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yiqing Xu
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China
| | - Yingzi Zhang
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China
| | - Yi Liu
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China
| | - Lei Guo
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China.
| | - Dongli Liu
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No.85, Wujin Road, Hongkou District, Shanghai, 200080, China.
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Ren Y, Fu S, Dong W, Chen J, Xue H, Bu W. The ncRNA-mediated regulatory networks of defensins and lysozymes in Riptortus pedestris: involvement in response to gut bacterial disturbances. Front Microbiol 2024; 15:1386345. [PMID: 38827147 PMCID: PMC11140134 DOI: 10.3389/fmicb.2024.1386345] [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: 02/15/2024] [Accepted: 04/23/2024] [Indexed: 06/04/2024] Open
Abstract
Insects depend on humoral immunity against intruders through the secretion of antimicrobial peptides (AMPs) and immune effectors via NF-κB transcription factors, and their fitness is improved by gut bacterial microbiota. Although there are growing numbers of reports on noncoding RNAs (ncRNAs) involving in immune responses against pathogens, comprehensive studies of ncRNA-AMP regulatory networks in Riptortus pedestris, which is one of the widely distributed pests in East Asia, are still not well understood under feeding environmental changes. The objective of this study employed the whole-transcriptome sequencing (WTS) to systematically identify the lncRNAs (long noncoding RNA) and circRNAs (circular RNA) and to obtain their differential expression from the R. pedestris gut under different feeding conditions. Functional annotation indicated that they were mainly enriched in various biological processes with the GO and KEGG databases, especially in immune signaling pathways. Five defensin (four novel members) and eleven lysozyme (nine novel members) family genes were identified and characterized from WTS data, and meanwhile, phylogenetic analysis confirmed their classification. Subsequently, the miRNA-mRNA interaction network of above two AMPs and lncRNA-involved ceRNA (competing endogenous RNA) regulatory network of one lysozyme were predicted and built based on bioinformatic prediction and calculation, and the expression patterns of differentially expressed (DE) defensins, and DE lysozymes and related DE ncRNAs were estimated and selected among all the comparison groups. Finally, to integrate the analyses of WTS and previous 16S rRNA amplicon sequencing, we conducted the Pearson correlation analysis to reveal the significantly positive or negative correlation between above DE AMPs and ncRNAs, as well as most changes in the gut bacterial microbiota at the genus level of R. pedestris. Taken together, the present observations provide great insights into the ncRNA regulatory networks of AMPs in response to rearing environmental changes in insects and uncover new potential strategies for pest control in the future.
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Affiliation(s)
- Yipeng Ren
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenhao Dong
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Juhong Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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Hou M, Wang Q, Zhang J, Zhao R, Cao Y, Yu S, Wang K, Chen Y, Ma Z, Sun X, Zhang Y, Li J. Differential Expression of miRNAs, lncRNAs, and circRNAs between Ovaries and Testes in Common Carp ( Cyprinus carpio). Cells 2023; 12:2631. [PMID: 37998366 PMCID: PMC10670750 DOI: 10.3390/cells12222631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
Female common carp grow faster than male individuals, implying that rearing females could be more profitable in aquaculture. Non-coding RNAs (ncRNAs) serve as versatile regulators with multiple functions in diverse biological processes. However, the roles of ncRNAs in the sex differentiation of common carp are less studied. In this study, we investigated the expression profiles of ncRNAs, including miRNAs, lncRNAs, and circRNAs, in the gonads to comprehend the roles of ncRNAs in sex differentiation in common carp. A substantial number of differentially expressed (DE) ncRNAs in ovaries and testes were identified. Some miRNAs, notably miR-205, miR-214, and miR-460-5p, might modulate hormone synthesis and thus maintain sex. A novel miRNA, novel_158, was predicted to suppress the expression of foxl3. DE lncRNAs were associated with oocyte meiosis, GnRH signaling pathways, and steroid biosynthesis, while DE circRNA target genes were enriched in the WNT signaling pathway and MAPK signaling pathway. We also analyzed ncRNA-mRNA interactions to shed light on the crosstalk between competing endogenous RNAs (ceRNAs), which is the critical mechanism by which lncRNAs and circRNAs function. Some lncRNAs and circRNAs may be able to competitively bind novel_313, a new miRNA, and thus regulate hsd17β3. Our research will provide a valuable resource for understanding the genetic basis of gonadal differentiation and development in common carp.
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Affiliation(s)
- Mingxi Hou
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Jin Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Yiming Cao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Shuangting Yu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
- Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kaikuo Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (K.W.); (Y.C.); (Z.M.)
| | - Yingjie Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (K.W.); (Y.C.); (Z.M.)
| | - Ziyao Ma
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; (K.W.); (Y.C.); (Z.M.)
| | - Xiaoqing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China; (M.H.); (Q.W.); (J.Z.); (R.Z.); (Y.C.); (S.Y.); (X.S.); (Y.Z.)
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Liu Q, Wang Y, Zhang T, Fang J, Meng S. Circular RNAs in vascular diseases. Front Cardiovasc Med 2023; 10:1247434. [PMID: 37840954 PMCID: PMC10570532 DOI: 10.3389/fcvm.2023.1247434] [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: 06/27/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Vascular diseases are the leading cause of morbidity and mortality worldwide and are urgently in need of diagnostic biomarkers and therapeutic strategies. Circular RNAs (circRNAs) represent a unique class of RNAs characterized by a circular loop configuration and have recently been identified to possess a wide variety of biological functions. CircRNAs exhibit exceptional stability, tissue specificity, and are detectable in body fluids, thus holding promise as potential biomarkers. Their encoding function and stable gene expression also position circRNAs as an excellent alternative to gene therapy. Here, we briefly review the biogenesis, degradation, and functions of circRNAs. We summarize circRNAs discovered in major vascular diseases such as atherosclerosis and aneurysms, with a particular focus on molecular mechanisms of circRNAs identified in vascular endothelial cells and smooth muscle cells, in the hope to reveal new directions for mechanism, prognosis and therapeutic targets of vascular diseases.
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Affiliation(s)
| | | | | | | | - Shu Meng
- Department of Basic Science Research, Guangzhou Laboratory, Guangzhou, China
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Zhang C, Huang Y, Gao X, Ren H, Gao S, Zhu W. Biological functions of circRNAs and their advance on skeletal muscle development in bovine. 3 Biotech 2023; 13:133. [PMID: 37096117 PMCID: PMC10121973 DOI: 10.1007/s13205-023-03558-3] [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: 02/11/2022] [Accepted: 01/10/2023] [Indexed: 04/26/2023] Open
Abstract
The development of skeletal muscle in animals is a complex biological process, which are strictly and precisely regulated by many genes and non-coding RNAs. Circular RNA (circRNA) was found as a novel class of functional non-coding RNA with ring structure in recent years, which appears in the process of transcription and is formed by covalent binding of single-stranded RNA molecules. With the development of sequencing and bioinformatics analysis technology, the functions and regulation mechanisms of circRNAs have attracted great attention due to its high stability characteristics. The role of circRNAs in skeletal muscle development have been gradually revealed, where circRNAs were involved in various biological processes, such as proliferation, differentiation, and apoptosis of skeletal muscle cells. In this review, we summarized the current studies advance of circRNAs involved in skeletal muscle development in bovine, and hope to gain a deeper understanding of the functional roles of the circRNAs in muscle growth. Our results will provide some theoretical supports and great helps for the genetic breeding of this species, and aiming at improving bovine growth and development and preventing muscle diseases.
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Affiliation(s)
- Cai Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Xiaochan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Hongtao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Shiyang Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023 China
| | - Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, 471023 China
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Yan S, Pei Y, Li J, Tang Z, Yang Y. Recent Progress on Circular RNAs in the Development of Skeletal Muscle and Adipose Tissues of Farm Animals. Biomolecules 2023; 13:biom13020314. [PMID: 36830683 PMCID: PMC9953704 DOI: 10.3390/biom13020314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Circular RNAs (circRNAs) are a highly conserved and specifically expressed novel class of covalently closed non-coding RNAs. CircRNAs can function as miRNA sponges, protein scaffolds, and regulatory factors, and play various roles in development and other biological processes in mammals. With the rapid development of high-throughput sequencing technology, thousands of circRNAs have been discovered in farm animals; some reportedly play vital roles in skeletal muscle and adipose development. These are critical factors affecting meat yield and quality. In this review, we have highlighted the recent advances in circRNA-related studies of skeletal muscle and adipose in farm animals. We have also described the biogenesis, properties, and biological functions of circRNAs. Furthermore, we have comprehensively summarized the functions and regulatory mechanisms of circRNAs in skeletal muscle and adipose development in farm animals and their effects on economic traits such as meat yield and quality. Finally, we propose that circRNAs are putative novel targets to improve meat yield and quality traits during animal breeding.
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Affiliation(s)
- Shanying Yan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Jiju Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- Correspondence: (Z.T.); (Y.Y.)
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- Correspondence: (Z.T.); (Y.Y.)
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Cai X, Gao C, Lymbery AJ, Armstrong NJ, Ma L, Li C. The immune-related circRNA-miRNA-mRNA ceRNA regulatory network in the liver of turbot (Scophthalmus maximus L.) induced by Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108506. [PMID: 36574792 DOI: 10.1016/j.fsi.2022.108506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Recently, Vibrio anguillarum, a Gram-negative pathogenic bacterium, has been becoming a major constraint on the development of the turbot aquaculture industry because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. Although the functions of protein-coding mRNAs in the immune response against bacterial infection have been reported, as well as several non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) and microRNAs (miRNAs), the relationships between mRNAs and ncRNAs in the immune system of turbot liver are still limited during bacterial infection. In present study, the comprehensive analyses of whole-transcriptome sequencing were conducted in turbot liver infected by V. anguillarum. The differential expression was analyzed in the data of circRNAs, miRNAs, and mRNAs. The interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted basing on the negative regulatory relationships between miRNAs and their target circRNAs\mRNAs. The circRNA-related ceRNA regulatory networks were constructed for the analyses of regulated mechanism in turbot immune system. Subsequently, the RT-qPCR was carried out to verify the results of sequencing. Finally, we identified 31 circRNAs, 53 miRNAs and 948 mRNAs with differential expression. Gene set enrichment analyses using Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that innate immunity was principally activated at the early stages of infection, while adaptive immunity was activated after 24 h. Finally, 65 circRNA-miRNA-mRNA pathways were constructed, based on the hypothesis of ceRNA regulatory networks. In conclusion, our findings provide new insights on the underlying immune response to bacterial infection and identify novel target genes for the prevention and control of disease in turbot.
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Affiliation(s)
- Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Alan J Lymbery
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Le Ma
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Cui J, Chen M, Zhang L, Huang S, Xiao F, Zou L. Circular RNAs: Biomarkers of cancer. CANCER INNOVATION 2022; 1:197-206. [PMID: 38089761 PMCID: PMC10686110 DOI: 10.1002/cai2.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/09/2022] [Indexed: 05/27/2024]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded closed RNAs that are produced by the back splicing of precursor mRNAs. The formation of circRNAs mainly involves intron-pairing-driven circularization, RNA-binding protein (RBP)-driven circularization, and lariat-driven circularization. The vast majority of circRNAs are found in the cytoplasm, and some intron-containing circRNAs are localized in the nucleus. CircRNAs have been found to function as microRNA (miRNA) sponges, interact with RBPs and translate proteins, and play an important regulatory role in the development and progression of cancer. CircRNAs exhibit tissue- and developmental stage-specific expression and are stable, with longer half-lives than linear RNAs. CircRNAs have great potential as biomarkers for cancer diagnosis and prognosis, which is highlighted by their detectability in tissues, especially in fluid biopsy samples such as plasma, saliva, and urine. Here, we review the current studies on the properties and functions of circRNAs and their clinical application value.
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Affiliation(s)
- Jingyi Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijing Hospital/National Center of Gerontology of National Health CommissionBeijingChina
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Meng Chen
- Key Laboratory for National Cancer Big Data Analysis and Implement, National Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lanxin Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Sida Huang
- Department of Public PolicyCornell UniversityIthacaNew YorkUSA
| | - Fei Xiao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijing Hospital/National Center of Gerontology of National Health CommissionBeijingChina
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Lihui Zou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijing Hospital/National Center of Gerontology of National Health CommissionBeijingChina
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11
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Li H, Xu L, Yi P, Li L, Yan T, Xie L, Zhu Z. High-throughput circular RNA sequencing reveals the profiles of circular RNA in non-cirrhotic hepatocellular carcinoma. BMC Cancer 2022; 22:857. [PMID: 35931993 PMCID: PMC9356431 DOI: 10.1186/s12885-022-09909-2] [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: 08/29/2021] [Accepted: 06/21/2022] [Indexed: 02/08/2023] Open
Abstract
Background Liver cirrhosis is a well-known risk factor for hepatocellular carcinoma (HCC). However, some HCC cases can also originate from non-cirrhotic livers. The aim of this study was to identify key circular RNAs (circRNAs) associated with the tumorigenesis of non-cirrhotic liver disease. Methods The differently expressed circRNAs between non-cirrhotic and cirrhotic HCCs were assessed with use of high-throughput circRNAs sequencing and validated with quantitative reverse transcription polymerase chain reaction (qRT-PCR). Potential biological functions of these dysregulated circRNAs were predicted with use of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A circRNA-miRNA-mRNA regulation network was constructed as achieved with use of miRanda software and visualized using Cytoscape software. Biological functions of the four most prominent dysregulated circRNAs identified were confirmed by in vitro experiments. Moreover, possible translations of these dysregulated circRNAs were also predicted. Results A total of 393 dysregulated circRNAs were identified between non-cirrhotic and cirrhotic HCC, including 213 that were significantly up-regulated and 180 significantly down-regulated circRNAs. Expression levels of the six most prominent dysregulated circRNAs were further validated using qRT-PCR. Many tumor related miRNAs were involved in the circRNA-miRNA-mRNA networks, including miR-182-5p, miR-561-3p, miR-125a-5p, miR-145, miR-23b-3p and miR-30e-3p, and downstream mRNAs of dysregulated circRNAs were significantly related with biological processes involved in the progression of tumors, including proliferation, migration, differentiation, and focal adhesion. Results from the in vitro experiments demonstrated that the most prominent dysregulated circRNAs exerted notable effects upon the proliferation and migration of HCC cells. Finally, we also identified 19 dysregulated circRNAs having potential for the coding of functional peptides. Conclusion The results of this present study indicate that circRNAs may play important roles in tumorigenesis of non-cirrhotic HCC. Such findings provide some novel insights and pave the way for the development of future studies directed at investigating the initiation and treatment of HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09909-2.
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Affiliation(s)
- Hongyu Li
- Department of Liver Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Liangliang Xu
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Pengsheng Yi
- Department of Hepato-Biliary-Pancreas, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, Sichuan Province, China
| | - Lian Li
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Tao Yan
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Liang Xie
- Department of Liver Surgery and Liver Transplantation Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhijun Zhu
- Department of Liver Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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12
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He Z, Ma Z, Yang D, Chen Q, He Z, Hu J, Deng F, Zhang Q, He J, Ye L, Chen H, He L, Huang X, Luo W, Yang S, Gu X, Zhang M, Yan T. Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus. BMC Genomics 2022; 23:552. [PMID: 35922747 PMCID: PMC9347082 DOI: 10.1186/s12864-022-08783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied. RESULTS Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT-PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. CONCLUSION Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou City Department of Agricultural and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qian Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiayang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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13
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Bai Y, Ding X, Liu Z, Shen J, Huang Y. Identification and functional analysis of circRNAs in the skeletal muscle of juvenile and adult largemouth bass (Micropterus salmoides). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100969. [PMID: 35150971 DOI: 10.1016/j.cbd.2022.100969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/06/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022]
Abstract
Circular RNA (circRNA) is a novel emerging type of endogenous regulatory non-coding RNA molecules with a covalent closed-loop configuration, which exerts important functions in multiple biological processes. CircRNAs are known to regulate gene expression as functional regulators interacting with miRNAs by sponge, which have been reported to regulate skeletal muscle development. Nevertheless, the information of circRNAs involved in regulating muscle growth and development in fish is largely unknown. Here, we first identified 312 and 511 circRNAs in skeletal muscle of juvenile and adult largemouth bass (LMB) using RNA sequencing, respectively. The differentially expressed circRNAs (DE-circRNAs) analysis showed that there are 44 DE-circRNAs at two different skeletal muscle growth stages. Six circRNAs were chosen randomly and their relative expression levels in juvenile and adult LMB were confirmed by real-time PCR, indicating that these circRNAs were existed authenticity. In addition, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis showed that these hose genes (their linear mRNAs) of DE-circRNAs were mainly enriched in the regulation of actin cytoskeleton signaling pathways. The circRNA-miRNA interaction regulatory networks indicated that one circRNA can regulate one or more miRNA. For instance, more than 30 miRNAs were regulated by two circRNAs (circRNA389 and circRNA399). Of them, the muscle-related miRNAs including the let-7 family, miR-133 and miR-26 and so on were found acting as miRNAs sponge regulated by circRNAs, indicating the roles of circRNAs in regulating muscle growth-related genes expression. Overall, these findings will not only broaden our understanding of circRNAs regulation mechanisms underlying muscle growth and development in LMB but also provides a novel clue for further functional research in carnivorous fish genetic breeding.
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Affiliation(s)
- Yuhe Bai
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Xinyu Ding
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Zezhong Liu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Junfei Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
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14
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Bin Li, Yan R, Liu X, Meng Z, Meng P, Wang Y, Huang Y. CircRNAs Biogenesis, Functions, and Its Research Progress in Aquaculture. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022020042] [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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15
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Niu M, Zou Q, Wang C. GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networks. Bioinformatics 2022; 38:2246-2253. [PMID: 35157027 DOI: 10.1093/bioinformatics/btac079] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/05/2021] [Accepted: 02/09/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION With the analysis of the characteristic and function of circular RNAs (circRNAs), people have realized that they play a critical role in the diseases. Exploring the relationship between circRNAs and diseases is of far-reaching significance for searching the etiopathogenesis and treatment of diseases. Nevertheless, it is inefficient to learn new associations only through biotechnology. RESULTS Consequently, we present a computational method, GMNN2CD, which employs a graph Markov neural network (GMNN) algorithm to predict unknown circRNA-disease associations. First, used verified associations, we calculate semantic similarity and Gaussian interactive profile kernel similarity (GIPs) of the disease and the GIPs of circRNA and then merge them to form a unified descriptor. After that, GMNN2CD uses a fusion feature variational map autoencoder to learn deep features and uses a label propagation map autoencoder to propagate tags based on known associations. Based on variational inference, GMNN alternate training enhances the ability of GMNN2CD to obtain high-efficiency high-dimensional features from low-dimensional representations. Finally, 5-fold cross-validation of five benchmark datasets shows that GMNN2CD is superior to the state-of-the-art methods. Furthermore, case studies have shown that GMNN2CD can detect potential associations. AVAILABILITY AND IMPLEMENTATION The source code and data are available at https://github.com/nmt315320/GMNN2CD.git.
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Affiliation(s)
- Mengting Niu
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China.,Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324000, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China.,Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang 324000, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, Heilongjiang 150000, China
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16
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Zhong H, Guo Z, Xiao J, Zhang H, Luo Y, Liang J. Comprehensive Characterization of Circular RNAs in Ovary and Testis From Nile Tilapia. Front Vet Sci 2022; 9:847681. [PMID: 35464370 PMCID: PMC9019548 DOI: 10.3389/fvets.2022.847681] [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: 01/03/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Circular RNA (circRNA) is an endogenous biomolecule in eukaryotes. It has tissue- and cell-specific expression patterns and can act as a microRNA sponge or competitive endogenous RNA. Although circRNA has been found in several species in recent years, the expression profiles in fish gonad are still not fully understood. We detected the expression of circRNA in the ovary, testis, and sex-changed gonad of tilapia by high-throughput deep sequencing, and circRNA-specific computing tools. A total of 20,607 circRNAs were obtained, of which 141 were differentially expressed in the testis and ovary. Among these circRNAs, 135 circRNAs were upregulated and 6 circRNAs were downregulated in female fish. In addition, GO annotation and KEGG pathway analysis of the host genes of circRNAs indicated that these host genes were mainly involved in adherens junction, androgen production, and reproductive development, such as ZP3, PLC, delta 4a, ARHGEF10, and HSD17b3. It is worth noting that we found that circRNAs in tilapia gonads have abundant miRNA-binding sites. Among them, 935 circRNAs have a regulatory effect on miR-212, 856 circRNAs have a regulatory effect on miR-200b-3p, and 529 circRNAs have a regulatory effect on miR-200b-5p. Thus, our findings provide a new evidence for circRNA–miRNA networks in the gonads in tilapia.
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Affiliation(s)
- Huan Zhong
- Hunan Research Center of Engineering Technology for Utilization of Distinctive Aquatic Resource, College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Zhongbao Guo
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Jun Xiao
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
- *Correspondence: Jun Xiao
| | - Hong Zhang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, China
| | - Yongju Luo
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Junneng Liang
- Guangxi Tilapia Genetic Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
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17
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Bao G, Zhao F, Wang J, Liu X, Hu J, Shi B, Wen Y, Zhao L, Luo Y, Li S. Characterization of the circRNA–miRNA–mRNA Network to Reveal the Potential Functional ceRNAs Associated With Dynamic Changes in the Meat Quality of the Longissimus Thoracis Muscle in Tibetan Sheep at Different Growth Stages. Front Vet Sci 2022; 9:803758. [PMID: 35433904 PMCID: PMC9011000 DOI: 10.3389/fvets.2022.803758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/23/2022] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) have a regulatory role in animal skeletal muscle development. In this study, RNA sequencing was performed to reveal the temporal regularity of circRNA expression and the effect of the circRNA–miRNA–mRNA ceRNA regulatory network on the meat quality of longissimus thoracis (LT) muscle in Tibetan sheep at different growth stages (4 months old, 4 m; 1.5 years old, 1.5 y; 3.5 years old, 3.5 y; 6 years old, 6 y). There were differences in the carcass performance and meat quality of Tibetan sheep at different ages. Especially, the meat tenderness significantly decreased (p < 0.05) with the increase of age. GO functional enrichment indicated that the source genes of the DE circRNAs were mainly involved in the protein binding, and myofibril and organelle assembly. Moreover, there was a significant KEGG enrichment in the adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway, as well as the calcium signaling pathway, regulating the pluripotency of the stem cells. The circRNA–miRNA–mRNA ceRNA interaction network analysis indicated that circRNAs such as circ_000631, circ_000281, and circ_003400 combined with miR-29-3p and miR-185-5p regulate the expression of LEP, SCD, and FASN related to the transformation of muscle fiber types in the AMPK signaling pathway. The oxidized muscle fibers were transformed into the glycolytic muscle fibers with the increase of age, the content of intramuscular fat (IMF) was lowered, and the diameter of the muscle fiber was larger in the glycolytic muscle fibers, ultimately increasing the meat tenderness. The study revealed the role of the circRNAs in the transformation of skeletal muscle fiber types in Tibetan sheep and its influence on meat quality. It improves our understanding of the role of circRNAs in Tibetan sheep muscle development.
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Affiliation(s)
- Gaoliang Bao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuliang Wen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Li Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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18
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Mei X, Chen SY. Circular RNAs in cardiovascular diseases. Pharmacol Ther 2022; 232:107991. [PMID: 34592203 PMCID: PMC8930437 DOI: 10.1016/j.pharmthera.2021.107991] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/08/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
In eukaryotes, precursor mRNAs (pre-mRNAs) produce a unique class of biologically active molecules namely circular RNAs (circRNAs) with a covalently closed-loop structure via back-splicing. Because of this unconventional circular form, circRNAs exhibit much higher stability than linear RNAs due to the resistance to exonuclease degradation and thereby play exclusive cellular regulatory roles. Recent studies have shown that circRNAs are widely expressed in eukaryotes and display tissue- and disease-specific expression patterns, including in the cardiovascular system. Although numerous circRNAs are discovered by in silico methods, a limited number of circRNAs have been studied. This review intends to summarize the current understanding of the characteristics, biogenesis, and functions of circRNAs and delineate the practical approaches for circRNAs investigation. Moreover, we discuss the emerging roles of circRNAs in cardiovascular diseases.
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Affiliation(s)
- Xiaohan Mei
- Departments of Surgery, University of Missouri School of Medicine, Columbia, MO, United States of America
| | - Shi-You Chen
- Departments of Surgery, University of Missouri School of Medicine, Columbia, MO, United States of America; Department of Medical Pharmacology & Physiology, University of Missouri School of Medicine, Columbia, MO, United States of America.
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19
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Wang P, Zhang Y, Deng L, Qu Z, Guo P, Liu L, Yu Z, Wang P, Liu N. The function and regulation network mechanism of circRNA in liver diseases. Cancer Cell Int 2022; 22:141. [PMID: 35361205 PMCID: PMC8973545 DOI: 10.1186/s12935-022-02559-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
Circular RNA (circRNA), a new type of endogenous non-coding RNA, is abundantly present in eukaryotic cells, and characterized as stable high conservation and tissue specific expression. It has been generated increasing attention because of their close association with the progress of diseases. The liver is the vital organ of humans, while it is prone to acute and chronic diseases due to the influence of multiple pathogenic factors. Moreover, hepatocellular carcinoma (HCC) is the one of most common cancer and the leading cause of cancer death worldwide. Overwhelming evidences indicate that some circRNAs are differentially expressed in liver diseases, such as, HCC, chronic hepatitis B, hepatic steatosis and hepatoblastoma tissues, etc. Additionally, these circRNAs are related to proliferation, invasion, migration, angiogenesis, apoptosis, and metastasis of cell in liver diseases and act as oncogenic agents or suppressors, and linked to clinical manifestations. In this review, we briefly summarize the biogenesis, characterization and biological functions, recent detection and identification technologies of circRNA, and regulation network mechanism of circRNA in liver diseases, and discuss their potential values as biomarkers or therapeutic targets for liver diseases, especially on HCC.
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Affiliation(s)
- Panpan Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 540001, People's Republic of China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China
| | - Yunhuan Zhang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, 475004, People's Republic of China
| | - Lugang Deng
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China
| | - Zhi Qu
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, 475004, People's Republic of China.
| | - Peisen Guo
- College of Public Health, Zhengzhou University, Zhengzhou, 540001, People's Republic of China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China
| | - Limin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 540001, People's Republic of China.,Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, 475004, People's Republic of China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, 540001, People's Republic of China.
| | - Peixi Wang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, 475004, People's Republic of China
| | - Nan Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 540001, People's Republic of China. .,Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, 475004, People's Republic of China. .,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China.
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20
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Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing. 3 Biotech 2022; 12:63. [PMID: 35186660 PMCID: PMC8825918 DOI: 10.1007/s13205-022-03132-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.
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Cao X, Xu X, Dong J, Xue Y, Sun L, Zhu Y, Liu T, Jin Q. Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. BMC Genomics 2022; 23:21. [PMID: 34983376 PMCID: PMC8725419 DOI: 10.1186/s12864-021-08184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive. Results Trichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration. Conclusions Our study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08184-y.
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Affiliation(s)
- Xingwei Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ying Xue
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
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Huo D, Sun L, Sun J, Lin C, Liu S, Zhang L, Yang H. Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 228:112994. [PMID: 34839139 DOI: 10.1016/j.ecoenv.2021.112994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Some sea cucumbers are economically and ecologically important, but they are threatened by thermal and hypoxic stress in changing oceanographic conditions. We construct circRNAs profiles, reveal circRNAs characters, and illustrate the potential regulatory roles of circRNAs in one commercially important species of sea cucumber, Apostichopus japonicus. Reads are distributed in intergenic (44.14%), exonic (48.26%) and intronic (7.60%) regions of the genome. A total of 1684 circRNAs were identified, and the most common spliced length is 269 nt in the present study. In three treatments (HT [thermal stress], LO [hypoxic stress], and HL [combined thermal and hypoxic stress]), 24, 27 and 27 differentially expressed (DE) circRNAs were identified, respectively. Five novel DE-circRNAs commonly occur in these treatments (novel_circ_0003311, novel_circ_0000229, novel_circ_0003944, novel_circ_0001458 and novel_circ_0000707), and based on them, potential circRNA-miRNA binding pairs were predicted. Sanger sequencing, RNase R treatment experiment and qPCR validation identified the accuracy of the circRNAs. Key circRNAs identified in the present study were covalently closed and were more stable under RNase R treatment than linear RNAs. Based on function analysis, circRNAs could regulate metabolic process, signal transduction, and ion responses in A. japonicus when exposed to thermal and hypoxic stress, and 'regulation of response to stimulus' is a common gene ontology (GO) term that is significantly enriched in each treatment; GO terms for 'DNA' and 'stress' are commonly enriched in heat-related treatments (HT and HL); and GO terms for 'protein' are commonly enriched in hypoxia-related treatments (LO and HL). When environmentally stressed, 'metabolism,' 'transport and catabolism,' 'membrane transport,' and 'signal transduction' were significantly responded in sea cucumber based on KEGG analysis. We provide insights into circRNA functions in stress regulation and lay a foundation for invertebrate circRNA research.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China.
| | - Jingchun Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Chenggang Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
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Wang G, Sun Q, Wang H, Liu H. Identification and characterization of circRNAs in the liver of blunt snout bream (Megalobrama amblycephala) infected with Aeromonas hydrophila. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104185. [PMID: 34174243 DOI: 10.1016/j.dci.2021.104185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Circular RNAs (circRNAs), a class of non-coding RNAs, play an important role in regulating various biological processes. In the present study, circRNAs from the Megalobrama amblycephala liver were identified at five different time points post Aeromonas hydrophila using RNA-seq technology. A total of 250 circRNAs were identified, of which 106 were differentially expressed (DE) in ten pairwise comparisons. GO and KEGG analyses showed that the parental genes of DE circRNAs were enriched in phagocytosis, complement and coagulation cascades, and Fc gamma R-mediated phagocytosis pathways. According to ceRNA hypothesis, the interaction network of circRNAs, miRNAs and mRNAs was constructed. Moreover, WGCNA was conducted, and five specific modules significantly related to bacterial infection were identified. All the above results reveal the important role of circRNAs in immune response, which enriches the information of circRNAs in teleost, and helps to understand the immune response mechanism of M. amblycephala to A. hydrophila.
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Affiliation(s)
- Guowen Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qianhui Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Huanling Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
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Wang L, You ZH, Li JQ, Huang YA. IMS-CDA: Prediction of CircRNA-Disease Associations From the Integration of Multisource Similarity Information With Deep Stacked Autoencoder Model. IEEE TRANSACTIONS ON CYBERNETICS 2021; 51:5522-5531. [PMID: 33027025 DOI: 10.1109/tcyb.2020.3022852] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Emerging evidence indicates that circular RNA (circRNA) has been an indispensable role in the pathogenesis of human complex diseases and many critical biological processes. Using circRNA as a molecular marker or therapeutic target opens up a new avenue for our treatment and detection of human complex diseases. The traditional biological experiments, however, are usually limited to small scale and are time consuming, so the development of an effective and feasible computational-based approach for predicting circRNA-disease associations is increasingly favored. In this study, we propose a new computational-based method, called IMS-CDA, to predict potential circRNA-disease associations based on multisource biological information. More specifically, IMS-CDA combines the information from the disease semantic similarity, the Jaccard and Gaussian interaction profile kernel similarity of disease and circRNA, and extracts the hidden features using the stacked autoencoder (SAE) algorithm of deep learning. After training in the rotation forest (RF) classifier, IMS-CDA achieves 88.08% area under the ROC curve with 88.36% accuracy at the sensitivity of 91.38% on the CIRCR2Disease dataset. Compared with the state-of-the-art support vector machine and K -nearest neighbor models and different descriptor models, IMS-CDA achieves the best overall performance. In the case studies, eight of the top 15 circRNA-disease associations with the highest prediction score were confirmed by recent literature. These results indicated that IMS-CDA has an outstanding ability to predict new circRNA-disease associations and can provide reliable candidates for biological experiments.
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Liu L, Chen Y, Diao J, Luo L, Gao Z. Identification and Characterization of Novel circRNAs Involved in Muscle Growth of Blunt Snout Bream ( Megalobrama amblycephala). Int J Mol Sci 2021; 22:ijms221810056. [PMID: 34576220 PMCID: PMC8467684 DOI: 10.3390/ijms221810056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Circular RNAs (circRNAs), a novel class of endogenous RNAs, have been recognized to play important roles in the growth of animals. However, the regulatory mechanism of circRNAs on fish muscle growth is still unclear. In this study, we performed whole transcriptome analysis of skeletal muscles from two populations with different growth rates (fast-growing and slow-growing) of blunt snout bream (Megalobrama amblycephala), an important fish species for aquaculture. The selected circRNAs were validated by qPCR and Sanger sequencing. Pairs of circRNA–miRNA–mRNA networks were constructed with the predicted differentially expressed (DE) pairs, which revealed regulatory roles in muscle myogenesis and hypertrophy. As a result, a total of 445 circRNAs were identified, including 42 DE circRNAs between fast-growing (FG) and slow-growing (SG) groups. Many of these DE circRNAs were related with aminoglycan biosynthetic and metabolic processes, cytokinetic processes, and the adherens junction pathway. The functional prediction results showed that novel_circ_0001608 and novel_circ_0002886, competing to bind with dre-miR-153b-5p and dre-miR-124-6-5p, might act as competing endogenous RNAs (ceRNAs) to control MamblycephalaGene14755 (pik3r1) and MamblycephalaGene10444 (apip) level, respectively, thus playing an important regulatory role in muscle growth. Overall, these results will not only help us to further understand the novel RNA transcripts in M. amblycephala, but also provide new clues to investigate the potential mechanism of circRNAs regulating fish growth and muscle development.
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Affiliation(s)
- Lifang Liu
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Yulong Chen
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jinghan Diao
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lifei Luo
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Correspondence: (L.L.); or (Z.G.); Tel.: +86-2787282113 (Z.G.); Fax: +86-2787282114 (Z.G.)
| | - Zexia Gao
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs/Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (L.L.); (Y.C.); (J.D.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
- Correspondence: (L.L.); or (Z.G.); Tel.: +86-2787282113 (Z.G.); Fax: +86-2787282114 (Z.G.)
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Jiang L, Wang X, Zhan X, Kang S, Liu H, Luo Y, Lin L. Advance in circular RNA modulation effects of heart failure. Gene 2021; 763S:100036. [PMID: 32793879 PMCID: PMC7412861 DOI: 10.1016/j.gene.2020.100036] [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: 06/04/2020] [Accepted: 07/21/2020] [Indexed: 12/25/2022]
Abstract
CircRNA (circular RNA) is a kind of closed circular structure of noncoding RNA molecules without 5′ hat structure and 3′ polyA, mainly located in the cytoplasm or stored in exosomes. It is not affected by RNA exonuclease, so it's stable and hard to be degraded. Proved to be widespread in a variety of eukaryotes, most circRNAs are cyclized by exons, some are lasso structures formed by intron cyclization. Recently, circRNAs have been demonstrated to play crucial roles in cardiomyocyte hypertrophy, fibrosis, autophagy and apoptosis, participating in the development of heart failure. There is increasing evidence that circRNAs may be a novel target for the treatment of heart failure.
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Affiliation(s)
- Li Jiang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Xiaoyan Wang
- Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Institute of Biomedical Science, Fudan University, 180 Feng Lin Road, Shanghai 200032, China
| | - Xiaopeng Zhan
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Sheng Kang
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Haibo Liu
- Department of Cardiology, Qingpu Branch of Zhongshan Hospital, Fudan University, 1158 Park East Road, Shanghai 201700, China
| | - Yu Luo
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Corresponding authors at: Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, China.
| | - Li Lin
- Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Corresponding authors at: Department of Cardiovascular Medicine, East Hospital, Tongji University School of Medicine, 150 Jimo Road, Shanghai 200120, China.
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Zhu M, Liang Z, Pan J, Zhang X, Xue R, Cao G, Hu X, Gong C. Hepatocellular carcinoma progression mediated by hepatitis B virus-encoded circRNA HBV_circ_1 through interaction with CDK1. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 25:668-682. [PMID: 34589285 PMCID: PMC8463320 DOI: 10.1016/j.omtn.2021.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) produces circular RNA (circRNA), whose functions have not yet been clearly elucidated. In this study, a novel circRNA HBV_circ_1 produced by HBV was identified in HBV-positive HepG2.2.15 cells and HBV-related hepatocellular carcinoma (HCC) tissue (HCCT). Microarray analysis of 68 HCCT samples showed that HBV_circ_1 abundance was significantly higher than that in paracancerous tissues. In addition, survival rate of HBV_circ_1-positive patients was significantly lower compared with HBV_circ_1-negative patients. Transient expression indicated that HBV_circ_1 enhanced cell proliferation, migration, and invasion and inhibited apoptosis in vitro. Furthermore, ectopical HBV_circ_1 expression increased tumor size in vivo. HBV_circ_1 was confirmed to interact with cyclin-dependent kinase 1 (CDK1) to regulate cell proliferation. These results suggest that HCC progression may be promoted by interaction of HBV_circ_1 with CDK1. Our data not only showed a novel clue to understand carcinogenesis and progress of HBV-related HCC but also provided a new target for the development of therapeutic drugs.
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Affiliation(s)
- Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Zi Liang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Jun Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Renyu Xue
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Guangli Cao
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
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Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis. BIOLOGY 2021; 10:biology10090830. [PMID: 34571707 PMCID: PMC8468179 DOI: 10.3390/biology10090830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 01/22/2023]
Abstract
Simple Summary CircRNAs: as molecules involved in gene regulation, have become a new research hotspot in the non-coding RNA field. CircRNAs show tissue- or developmental stage-specific patterns of expression and can influence the expression levels of their parental genes. Recent studies have documented the potential biological roles of circRNAs in the growth, development, reproduction and health of humans and animals. Tongue sole (Cynoglossus semilaevis) is a marine flatfish that is an economically important farmed species in China. The commercial aquaculture of tongue sole has developed in the last few years because wild resources have decreased. Reproduction is regulated by brain-pituitary-gonad-liver axis which limits the development of artificial tongue sole culture. However, the roles of circRNAs in the ovarian development and maturation of tongue sole has never been reported. The identification of the potential functions of circRNAs provides a foundation for understanding the genetic mechanisms that regulate oocyte growth and maturation, which will allow the efficiency of tongue sole reproduction to be improved. Moreover, our findings extend the knowledge about a new type of endogenous RNA involved in regulating the ovarian development and maturation of tongue sole. Abstract CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative abundances of circRNAs in tongue sole tissues during three ovarian developmental stages. We detected 6790 circRNAs in the brain, 5712 in the pituitary gland, 4937 in the ovary and 4160 in the liver. Some circRNAs exhibit tissue-specific expression, and qRT-PCR largely confirmed 6 differentially expressed (DE) circRNAs. Gene Ontology and KEGG pathway analyses of DE mRNAs were performed. Some DE circRNA parental genes were closely associated with biological processes in key signalling pathways and may play essential roles in ovarian development and maturation. We found that the selected circRNAs were involved in 10 pathways. RNase R digestion experiment and Sanger sequencing verified that the circRNA had a ring structure and was RNase R resistant. qRT-PCR results largely confirmed differential circRNA expression patterns from the RNA-seq data. These findings indicate that circRNAs are widespread in terms of present in production-related tissues of tongue sole with potentially important regulatory roles in ovarian development and maturation.
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Wu M, Peng D, Zhong X. Exploration of Circular RNA Interactomes by RNA Pull-Down Method. Methods Mol Biol 2021; 2372:203-208. [PMID: 34417754 DOI: 10.1007/978-1-0716-1697-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Circular RNAs (circRNAs) are endogenous RNA molecules produced by back-splicing during the maturation process of mRNA precursors. Recent research revealed circRNAs as important regulators in a variety of physiological and pathological processes. However, the biological functions of circRNAs remains largely unknown. The RNA pull-down method can specifically and efficiently enrich circRNAs and their interacting partners. In order to further characterize the functions and working mechanism of circRNAs, here we provide a detailed RNA pull-down protocol for capturing and identifying the interactomes of circRNAs.
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Affiliation(s)
- Mengshi Wu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Center for Stem Cell Biology and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Dan Peng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Center for Stem Cell Biology and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xiaomin Zhong
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Center for Stem Cell Biology and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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Chao F, Wang S, Zhang C, Han D, Xu G, Chen G. The Emerging Role of Circular RNAs in Prostate Cancer: A Systematic Review. Front Cell Dev Biol 2021; 9:681163. [PMID: 34386491 PMCID: PMC8353182 DOI: 10.3389/fcell.2021.681163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Prostate cancer is one of the most common malignant tumors that threaten the health of men. It is urgent to explore new molecular targets and develop new drugs for the treatment of prostate cancer. Circular RNAs (circRNAs) are aberrantly expressed in various malignant tumors. The dysregulated circRNAs are involved in the metastasis, tumor growth, drug resistance, and immunosuppression of malignant tumors. The present review systematically summarized publications concerning the biological implications of circRNAs in prostate cancer. The PubMed and Web of Science databases were used to retrieve publications concerning circRNAs and prostate cancer until June 16, 2021. The following keywords were used in the literature search: (circRNA OR circular RNA) AND prostate cancer. 73 publications were enrolled in the present systematic review to summarize the role of circRNAs in prostate cancer. The dysregulated and functional circRNAs were involved in the cell cycle, proliferation, migration, invasion, metastasis, drug resistance and radiosensitivity of prostate cancer. In addition, circRNAs could function through EVs and serve as prognostic and diagnostic biomarkers. Certain circRNAs were correlated with clinicopathological features of prostate cancer. A comprehensive review of the molecular mechanism of the tumorigenesis and progression of prostate cancer may contribute to the development of new therapies of prostate cancer in the future.
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Affiliation(s)
- Fan Chao
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Shiyu Wang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai, China
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan University, Shanghai, China
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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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Li M, Zhang N, Zhang W, Hei W, Cai C, Yang Y, Lu C, Gao P, Guo X, Cao G, Li B. Comprehensive analysis of differentially expressed circRNAs and ceRNA regulatory network in porcine skeletal muscle. BMC Genomics 2021; 22:320. [PMID: 33932987 PMCID: PMC8088698 DOI: 10.1186/s12864-021-07645-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially expressed circRNAs (DEcircRNAs), as well as the DEcircRNA-miRNA-mRNA regulatory network, at different stages of porcine skeletal muscle development. Here, we present a panoramic view of circRNA expression in porcine skeletal muscle from Large White and Mashen pigs at 1, 90, and 180 days of age. RESULTS We identified a total of 5819 circRNAs. DEcircRNA analysis at different stages showed 327 DEcircRNAs present in both breeds. DEcircRNA host genes were concentrated predominately in TGF-β, MAPK, FoxO, and other signaling pathways related to skeletal muscle growth and fat deposition. Further prediction showed that 128 DEcircRNAs could bind to 253 miRNAs, while miRNAs could target 945 mRNAs. The constructed ceRNA network plays a vital role in skeletal muscle growth and development, and fat deposition. Circ_0015885/miR-23b/SESN3 in the ceRNA network attracted our attention. miR-23b and SESN3 were found to participate in skeletal muscle growth regulation, also playing an important role in fat deposition. Using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR, circ_0015885, an exonic circRNA derived from Homer Scaffold Protein 1 (HOMER1), was confirmed to be differentially expressed during skeletal muscle growth. In summary, circ_0015885 may further regulate SESN3 expression by interacting with miR-23b to function in skeletal muscle. CONCLUSIONS This study not only enriched the circRNA library in pigs, but also laid a solid foundation for the screening of key circRNAs during skeletal muscle growth and intramural fat deposition. In addition, circ_0015885/miR-23b/SESN3, a new network regulating skeletal muscle growth and fat deposition, was identified as important for increasing the growth rate of pigs and improving meat quality.
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Affiliation(s)
- Meng Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Na Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Wanfeng Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Wei Hei
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Yang Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
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Li SY, Wang CY, Xiao YX, Tang XB, Yuan ZW, Bai YZ. RNA-Seq Profiling of Circular RNAs During Development of Hindgut in Rat Embryos With Ethylenethiourea-Induced Anorectal Malformations. Front Genet 2021; 12:605015. [PMID: 33927745 PMCID: PMC8076906 DOI: 10.3389/fgene.2021.605015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/26/2021] [Indexed: 12/26/2022] Open
Abstract
Anorectal malformations (ARMs) are among the most common congenital terminal digestive tract malformations. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play roles in the development of the digestive system; however, their contributions to the pathogenesis of ARMs are not well-established. In this study, we explored the mechanism underlying ethylenethiourea (ETU)-induced ARMs by profiling circRNA expression via RNA-seq and constructing a regulatory circRNA-miRNA-mRNA network. Nine pregnant rats were gavage-fed a single dose of 125 mg/kg 1% ETU (ARM group) on gestational day 10 (GD10), and another 9 pregnant rats received a similar dose of saline (normal group) as a control. Embryos were obtained by cesarean section on the key time-points of anorectal development (GD14, GD15, and GD16). Hindgut samples isolated from the fetuses were evaluated by high-throughput sequencing and differentially expressed circRNAs were validated by reverse transcription-quantitative polymerase chain reaction, agarose gel electrophoresis, and Sanger cloning and sequencing. A total of 18295 circRNAs were identified in the normal and ARM groups. Based on the 425 differentially expressed circRNAs (|Fc| > 2, p < 0.05), circRNA-miRNA and miRNA-mRNA pairs were predicted using miREAP, miRanda, and TargetScan. A total of 55 circRNAs (14 up- and 41 downregulated in the ARM group compared to the normal group) were predicted to bind to 195 miRNAs and 947 mRNAs. Competing endogenous RNA networks and a Kyoto Encyclopedia of Genes and Genomes analysis revealed that novel_circ_001042 had the greatest connectivity and was closely related to ARM-associated signaling pathways, such as the Wingless Type MMTV integration site family, mitogen-activated protein kinase, and transforming growth factor-β pathways. These results provide original insight into the roles of circRNAs in ARMs and provide a valuable resource for further analyses of molecular mechanisms and signaling networks.
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Affiliation(s)
- Si Ying Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Yi Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yun Xia Xiao
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Bing Tang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zheng Wei Yuan
- The Key Laboratory of Health Ministry for Congenital Malformation, Shenyang, China
| | - Yu Zuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
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Zhang Y, Zhong Y, Guo S, Zhu Y, Guo J, Fu Y, Li M. CircRNA profiling reveals circ880 functions as miR-375-3p sponge in medaka gonads. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100797. [PMID: 33714082 DOI: 10.1016/j.cbd.2021.100797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/25/2020] [Accepted: 01/23/2021] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) have been regarded as regulators in the biological processes of various species. However, there is no report about circRNAs in the gonads of model fish medaka (Oryzias latipes). In this study, 1157 and 1570 circRNAs were obtained in the ovary and testis by RNA-sequencing. The characteristics of circRNAs were explored in sequence length, exon composition, and chromosome position. 24 circRNAs were significantly up or down-regulated in the testis compared to the ovary, 9 of which were verified by qRT-PCR. Interestingly, circ452 was highly expressed in the testis while circ880 expression exhibited sexual dimorphism. In situ hybridization (ISH) revealed that circ452 and circ880 were expressed in meiotic germ cells, and circ880 was also abundant in spermatogonia. In addition, dual-luciferase reporter assay manifested that circ880 and Oldnd can combine with miR-375-3p. Overall, these results provide emerging circRNA libraries and open new avenues for future investigation of circRNAs in medaka.
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Affiliation(s)
- Yu Zhang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ying Zhong
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Shaoyu Guo
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yefei Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jing Guo
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| | - Mingyou Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
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Identification of Circular RNAs in Hypothalamus of Gilts during the Onset of Puberty. Genes (Basel) 2021; 12:genes12010084. [PMID: 33445426 PMCID: PMC7827264 DOI: 10.3390/genes12010084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/09/2023] Open
Abstract
The disorders of puberty have shown negative outcomes on health of mammals, and the hypothalamus is thought to be the main regulator of puberty by releasing GnRH. Many studies show that the circular RNAs (circRNAs) might be implicated in the timing of puberty in mammals. However, the circRNAs in the hypothalamus of gilts have not been explored. To profile the changes and biological functions of circRNAs in the hypothalamus during the onset of puberty, RNA-seq was utilized to establish pre-, in-, and post-pubertal hypothalamic circRNAs profiles. In this study, the functions of hypothalamic circRNAs were enriched in the signaling pathway of neurotrophin, progesterone-mediated oocyte maturation, oocyte meiosis, insulin, ErbB, and mTOR, which have been highly suggested to be involved in the timing of puberty. Furthermore, 53 circRNAs were identified to be putative hypothalamus-specific expressed circRNAs, and some of them were exclusively expressed in the one of three pubertal stages. Moreover, 22 differentially expressed circRNAs were identified and chosen to construct the circRNA-miRNA-gene network. Moreover, 10 circRNAs were found to be driven by six puberty-related genes (ESR1, NF1, APP, ENPP2, ARNT, and DICER1). Subsequently, the expression changes of several circRNAs were confirmed by RT-qPCR. Collectively, the preliminary results of hypothalamic circRNAs provided useful information for the investigation of the molecular mechanism for the timing of puberty in gilts.
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Quan J, Kang Y, Luo Z, Zhao G, Li L, Liu Z. Integrated analysis of the responses of a circRNA-miRNA-mRNA ceRNA network to heat stress in rainbow trout (Oncorhynchus mykiss) liver. BMC Genomics 2021; 22:48. [PMID: 33430762 PMCID: PMC7802223 DOI: 10.1186/s12864-020-07335-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 12/22/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the intensification of global warming, rainbow trout (Oncorhynchus mykiss) suffer from varying degrees of thermal stimulation, leads to mass mortality, which severely restrict the development of aquaculture. Understanding the molecular regulatory mechanisms of rainbow trout under heat stress is useful to develop approaches to relieve symptoms. RESULTS Changes in nonspecific immune parameters revealed that a strong stress response was caused in rainbow trout at 24 °C, so we performed multiple transcriptomic analyses of rainbow trout liver under heat stress (HS, 24 °C) and control conditions (CG, 18 °C). A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified. A ceRNA regulatory network was constructed and a total of 301 circRNA-miRNA and 51 miRNA-mRNA negative correlation pairs were screened, and three regulatory correlation pairs were predicted: novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some target genes involved in metabolic processes, biological regulation or response to stimulus were highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as protein processing in the ER, the estrogen signaling pathway, and the HIF-1 signaling pathway. CONCLUSIONS These results extend our understanding of the molecular mechanisms of the heat stress response and provide novel insight for the development of strategies that relieve heat stress.
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Affiliation(s)
- Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Yujun Kang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Zhicheng Luo
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
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Zhang H, Liu S, Li X, Yao L, Wu H, Baluška F, Wan Y. An Antisense Circular RNA Regulates Expression of RuBisCO Small Subunit Genes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:665014. [PMID: 34108983 PMCID: PMC8181130 DOI: 10.3389/fpls.2021.665014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/06/2021] [Indexed: 05/17/2023]
Abstract
Circular RNA (circRNA) is a novel class of endogenous long non-coding RNA (lncRNA) and participates in diverse physiological process in plants. From the dataset obtained by high-throughput RNA sequencing, we identified a circRNA encoded by the sense strand of the exon regions spanning two RuBisCO small subunit genes, RBCS2B and RBCS3B, in Arabidopsis thaliana. We further applied the single specific primer-polymerase chain reaction (PCR) and Sanger sequencing techniques to verify this circRNA and named it ag-circRBCS (antisense and across genic-circular RNA RBCS). Using quantitative real-time PCR (qRT-PCR), we found that ag-circRBCS shares a similar rhythmic expression pattern with other RBCS genes. The expression level of ag-circRBCS is 10-40 times lower than the expression levels of RBCS genes in the photosynthetic organs in Arabidopsis, whereas the Arabidopsis root lacked ag-circRBCS expression. Furthermore, we used the delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to deliver in vitro synthesized ag-circRBCS into Arabidopsis seedlings. Our results indicate that ag-circRBCS could significantly depress the expression of RBCS. Given that ag-circRBCS was expressed at low concentration in vivo, we suggest that ag-circRBCS may represent a fine-tuning mechanism to regulating the expression of RBCS genes and protein content in Arabidopsis.
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Affiliation(s)
- He Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shuai Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Xinyu Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Lijuan Yao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Hongyang Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - František Baluška
- Institute of Molecular and Cellular Botany, Bonn University, Bonn, Germany
| | - Yinglang Wan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yinglang Wan
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Wei G, Zhu J, Hu HB, Liu JQ. Circular RNAs: Promising biomarkers for cancer diagnosis and prognosis. Gene 2020; 771:145365. [PMID: 33346098 DOI: 10.1016/j.gene.2020.145365] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/23/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs), a group of non-coding RNA characterized by the presence of covalent bonds linking 3' and 5' ends, act as miRNA sponges to participate in the tumorigenesis. Being stable, conserved and cell- or tissue-specific, circRNAs have shown their potentials as molecular markers for cancer. Convenient and noninvasive approaches may be developed based on the roles of circRNAs to diagnose or predict the prognosis of tumors. Although most of the potential mechanisms are not entirely clear, circRNAs have shown a universal and critical role in regulating cellular processes of cancers. This review summarized the classification, formation, characteristics, detection, and biological functions of circRNAs. We proposed the possibility of using circRNAs as biomarkers for cancer diagnosis, treatment and prognosis.
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Affiliation(s)
- Guohao Wei
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Sparkfire Scientific Research Group, Nanjing Medical University, Nanjing, China
| | - Jing Zhu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Sparkfire Scientific Research Group, Nanjing Medical University, Nanjing, China
| | - Hai-Bo Hu
- Department of Thoracic Surgery, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China.
| | - Jia-Qiang Liu
- Department of Oral and CranioMaxillofacial, Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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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: 15] [Impact Index Per Article: 3.8] [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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Wang Z, Zhang Y, Dai K, Liang Z, Zhu M, Zhang M, Pan J, Hu X, Zhang X, Xue R, Cao G, Gong C. circEgg regulates histone H3K9me3 by sponging bmo-miR-3391-5p and encoding circEgg-P122 protein in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 124:103430. [PMID: 32585305 DOI: 10.1016/j.ibmb.2020.103430] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/19/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
A large number of circular RNAs (circRNAs) have been found in different organisms; however, their function in the regulation of histone modification remains unknown. In this study, we found that the circRNA circEgg, cyclized by the 9th-13th exon of Bombyx mori histone-lysine N-methyltransferase eggless (BmEgg) gene, mainly distributes in the cytoplasm, its expression levels changed with silkworm developmental stages, and the linear transcript level of the BmEgg gene was decreased when circEgg was overexpressed. Moreover, circEgg was found to repress histone H3 lysine 9 methylation (H3K9me3), promote histone H3 lysine 9 acetylation (H3K9ac), and positively regulate histone deacetylase (HDAC) Rpd3 (BmHDAC Rpd3) gene expression by sponging the microRNA bmo-miR-3391-5p. Furthermore, circEgg encodes a circEgg-P122 protein which appears to inhibit H3K9me3. These results suggest that circEgg regulates histone modification by sponging bmo-miR-3391-5p and encoding circEgg-P122 protein. To our knowledge, this is the first report showing that a circRNA produced by BmEgg plays an important role in histone epigenetic modification.
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Affiliation(s)
- Zhangyan Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Yunshan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Kun Dai
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zi Liang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Min Zhu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Mingtian Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jun Pan
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xiaolong Hu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Xing Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Renyu Xue
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Guangli Cao
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China
| | - Chengliang Gong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China; Agricultural Biotechnology Research Institute, Agricultural Biotechnology and Ecological Research Institute, Soochow University, Suzhou, 215123, China.
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Shen Y, Liang W, Lin Y, Yang H, Chen X, Feng P, Zhang B, Zhu J, Zhang Y, Luo H. Single molecule real-time sequencing and RNA-seq unravel the role of long non-coding and circular RNA in the regulatory network during Nile tilapia (Oreochromis niloticus) infection with Streptococcus agalactiae. FISH & SHELLFISH IMMUNOLOGY 2020; 104:640-653. [PMID: 32544555 DOI: 10.1016/j.fsi.2020.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The tilapia aquaculture industry is facing heavy economic losses due to Streptococcus agalactiae (S. agalactiae) infections. While progress has been made in past years, the lack of a high-quality tilapia genome and transcript annotations makes systematic and comprehensive exploration for a non-coding RNA regulatory network associated with the infection process unfeasible, and it stunts further research focused on disease defense and treatment. Herein, single molecular real time sequencing (SMRT-Seq) and RNA-seq data were utilized to generate a high-quality transcript annotation. In addition, Changes in mRNA and non-coding RNA expression were also analyzed during a S. agalactiae infection in tilapia. FINDINGS In total, 16.79 Gb of clean data were obtained by sequencing on six SMRT cells, with 712,294 inserts (326,645 full-length non-chimeric reads and 354,188 non-full-length reads). A total of 197,952 consensus transcripts were obtained. Additionally, 55,857 transcript sequences were acquired, with 12,297 previously annotated and 43,560 newly identified transcripts. To further examine the immune response in Oreochromis niloticus following a S. agalactiae infection, a total of 470.62 Gb of clean data was generated by sequencing a library containing 18 S. agalactiae infected tilapia samples. Of the identified genes, 9911 were newly exploited, of which 7102 were functional annotated. Furthermore, 7874 mRNAs, 1281 long non-coding RNAs (out of 21,860 long non-coding RNAs), and 61 circular RNAs (out of 1026 circular RNAs) were found to be differentially expressed during infection, with the 1026 circRNAs not previously identified in tilapia. Moreover, k-means clustering and WGCNA analyses revealed that the immune response of tilapia to a S. agalactiae infection can be divided into three stages: cytokines driven rapid immune response, energy metabolism promotion, and the production of lysosomes and phagosomes. During this response, the head kidney and spleen have synergistic effects, while maintaining independent characteristics. Finally, lncRNA-mRNA (trans and cis), lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA regulatory networks were constructed and revealed that non-coding RNA is involved in the regulation of immune-related genes. CONCLUSIONS This study generated a greatly-improved transcript annotation for tilapia using long-read PacBio sequencing technology, and revealed the presence of a regulatory network comprised of non-coding RNAs in Nile tilapia infected with S. agalactiae.
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Affiliation(s)
- Yudong Shen
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Wanwen Liang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Huizan Yang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Xiaohan Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Pengfei Feng
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Bin Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Jiajie Zhu
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China
| | - Yongde Zhang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China.
| | - Honglin Luo
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, Guangxi, 530021, PR China.
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FcircSEC: An R Package for Full Length circRNA Sequence Extraction and Classification. Int J Genomics 2020; 2020:9084901. [PMID: 32566642 PMCID: PMC7285417 DOI: 10.1155/2020/9084901] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/02/2020] [Accepted: 02/28/2020] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are formed by joining the 3′ and 5′ ends of RNA molecules. Identification of circRNAs is an important part of circRNA research. The circRNA prediction methods can predict the circRNAs with start and end positions in the chromosome but cannot identify the full-length circRNA sequences. We present an R package FcircSEC (Full Length circRNA Sequence Extraction and Classification) to extract the full-length circRNA sequences based on gene annotation and the output of any circRNA prediction tools whose output has a chromosome, start and end positions, and a strand for each circRNA. To validate FcircSEC, we have used three databases, circbase, circRNAdb, and plantcircbase. With information such as the chromosome and strand of each circRNA as the input, the identified sequences by FcircSEC are consistent with the databases. The novelty of FcircSEC is that it can take the output of state-of-the-art circRNA prediction tools as input and is applicable for human and other species. We also classify the circRNAs as exonic, intronic, and others. The R package FcircSEC is freely available.
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The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat Rev Mol Cell Biol 2020; 21:475-490. [PMID: 32366901 DOI: 10.1038/s41580-020-0243-y] [Citation(s) in RCA: 848] [Impact Index Per Article: 212.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Many protein-coding genes in higher eukaryotes can produce circular RNAs (circRNAs) through back-splicing of exons. CircRNAs differ from mRNAs in their production, structure and turnover and thereby have unique cellular functions and potential biomedical applications. In this Review, I discuss recent progress in our understanding of the biogenesis of circRNAs and the regulation of their abundance and of their biological functions, including in transcription and splicing, sequestering or scaffolding of macromolecules to interfere with microRNA activities or signalling pathways, and serving as templates for translation. I further discuss the emerging roles of circRNAs in regulating immune responses and cell proliferation, and the possibilities of applying circRNA technologies in biomedical research.
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45
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Zhang Y, Lin X, Geng X, Shi L, Li Q, Liu F, Fang C, Wang H. Advances in circular RNAs and their role in glioma (Review). Int J Oncol 2020; 57:67-79. [PMID: 32319596 PMCID: PMC7252450 DOI: 10.3892/ijo.2020.5049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Glioma is the most common primary tumour of the central nervous system, and is associated with a high postoperative recurrence rate and resistance to chemotherapy. High‑grade glioblastoma in particular has a very poor prognosis and poses a serious threat to human health. Related studies have confirmed that the occurrence and development of gliomas are closely associated with the abnormal expression and regulation of genes. Moreover, the number of studies on the association of the expression of non‑coding RNAs [linear RNAs, microRNAs and circular RNAs (circRNAs)] in human cells with glioma has been gradually increasing in recent years. Among those, circRNAs, previously considered to be 'splicing errors', have been shown to be highly expressed in eukaryotic cells and regulate the biological behaviour of gliomas. circRNAs are highly abundant and stable, and have become a research hotspot in the field of glioma molecular biology. The aim of the present review was to focus on the research progress regarding the association between circRNA expression and gliomas, and to provide a theoretical basis according to the currently available literature for further exploring this association. The present study may be of value for the early diagnosis, pathological grading, targeted therapy and prognostic evaluation of gliomas.
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Affiliation(s)
- Yuhao Zhang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Xiaomeng Lin
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Xiuchao Geng
- Hebei University of Chinese Medicine, Faculty of Integrated Traditional Chinese and Western Medicine, Shijiazhuang, Hebei 050091, P.R. China
| | - Liang Shi
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Qiang Li
- Hebei University of Chinese Medicine, Faculty of Acupuncture‑Moxibustion and Tuina, Shijiazhuang, Hebei 050200, P.R. China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Hong Wang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
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46
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Zhang MJ, Yin JW, Wu JH, Gu J, Yuan CY, Miao HJ, Yu ZB. Circular RNAs are abundant and dynamically expressed during the embryonic lung development of C57BL/6 mice. Heliyon 2020; 6:e03437. [PMID: 32154408 PMCID: PMC7058915 DOI: 10.1016/j.heliyon.2020.e03437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/16/2020] [Accepted: 02/14/2020] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs), a novel type of endogenous RNAs, can function as microRNA (miRNA) sponges capable of regulating gene transcription, binding to RNA-associated proteins, and even encoding proteins. CircRNAs are involved in various cell behaviors, such as proliferation and apoptosis. The mouse model has also been demonstrated to be similar to that of humans in many studies. To explore the profile of circRNAs during embryonic lung development and their potential functions in lung development-related diseases, mouse embryos at the pseudoglandular phase, canalicular phase, saccular phase, and alveolar phase were collected. High-throughput sequencing was then used to identify a total of 1,735 circRNAs (junction reads ≥5 and p < 0.05). It is well known that the functions of circRNAs are related to host genes. In our study, bioinformatics analysis indicated that the screened host genes were closely associated with lung development and included the Hippo signaling pathway, PI3K-Akt signaling pathways, and TGF-β signaling pathways. Moreover, miRNA sponges are another mechanism involved in lung development. Therefore, we predicted many miRNAs binding to circRNAs, such as miR-17 and miR-20, using the TargetScan and miRanda databases. Previously, miRNAs were proven to be necessary for lung development. The peak expression of circRNAs is distributed at different time points, suggesting their involvement in different stages of embryonic mouse lung development.
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Affiliation(s)
- Meng-Jie Zhang
- Department of Emergency, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Jiang-Wen Yin
- Department of Emergency, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Jin-Huan Wu
- Department of Emergency, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Jie Gu
- Department of Emergency, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Cai-Yun Yuan
- Department of Pediatrics, Nantong Maternal and Child Health Care Hospital, Nantong, Jiangsu, 226000, China
| | - Hong-Jun Miao
- Department of Emergency, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Zhang-Bin Yu
- Department of Pediatrics, The Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, 210004, China
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Sun J, Li B, Shu C, Ma Q, Wang J. Functions and clinical significance of circular RNAs in glioma. Mol Cancer 2020; 19:34. [PMID: 32061256 PMCID: PMC7023692 DOI: 10.1186/s12943-019-1121-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022] Open
Abstract
CircRNAs are a class of single-stranded RNA molecules with a covalently closed loop structure and have been characterized by high stability, abundance, conservation, and display tissue/developmental stage-specific expression, furthermore, based on the abundance in distinct body fluids or exosomes, circRNAs present novel biomarkers and targets for the diagnosis and prognosis of cancers. Recently, the regulatory mechanisms of biogenesis and molecular functions, including miRNAs and RBPs sponge, translation as well as transcriptional and splicing regulation, have been gradually uncovered, although various aspects remained to be elucidated in combination with deep-sequence and bioinformatics. Accumulating studies have indicated that circRNAs are more enriched in neuronal tissues partly due to the abundance of specific genes promoting circularization, suggesting dysregulation of circRNAs is closely related to diseases of the nervous system, including glioma. In this review, we elaborate on the biogenesis, functions, databases as well as novel advances especially involved in the molecular pathways, highlight its great value as diagnostic or therapeutic targets in glioma.
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Affiliation(s)
- Jikui Sun
- School of Medicine, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, People's Republic of China.,Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China
| | - Banban Li
- Qilu Hospital, Shandong University, 107 Cultural West Road, Jinan, 250012, People's Republic of China.,Department of Hematology, Taian Central Hospital, 29 Longtan Road, Taian, 271000, People's Republic of China
| | - Chang Shu
- Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China
| | - Quanfeng Ma
- Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China
| | - Jinhuan Wang
- School of Medicine, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, People's Republic of China. .,Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China.
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48
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Zhang Q, Wang W, Zhou Q, Chen C, Yuan W, Liu J, Li X, Sun Z. Roles of circRNAs in the tumour microenvironment. Mol Cancer 2020; 19:14. [PMID: 31973726 PMCID: PMC6977266 DOI: 10.1186/s12943-019-1125-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/26/2019] [Indexed: 02/06/2023] Open
Abstract
The tumour microenvironment (TME) constitutes the area surrounding the tumour during its development and has been demonstrated to play roles in cancer-related diseases through crosstalk with tumour cells. Circular RNAs (circRNAs) are a subpopulation of endogenous noncoding RNAs (ncRNAs) that are ubiquitously expressed in eukaryotes and have multiple biological functions in the regulation of cancer onset and progression. An increasing number of studies have shown that circRNAs participate in the multifaceted biological regulation of the TME. However, details on the mechanisms involved have remained elusive until now. In this review, we analyse the effects of circRNAs on the TME from various perspectives, including immune surveillance, angiogenesis, hypoxia, matrix remodelling, exo-circRNAs and chemoradiation resistance. Currently, the enormous potential for circRNA use in targeted therapy and as noninvasive biomarkers have drawn our attention. We emphasize the prospect of targeting circRNAs as an essential strategy to regulate TME, overcome cancer resistance and improve therapeutic outcomes.
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Affiliation(s)
- Qiuge Zhang
- Department of Geriatric Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chen Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Xiaoli Li
- Department of Geriatric Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. .,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China.
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49
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Guria A, Sharma P, Natesan S, Pandi G. Circular RNAs-The Road Less Traveled. Front Mol Biosci 2020; 6:146. [PMID: 31998746 PMCID: PMC6965350 DOI: 10.3389/fmolb.2019.00146] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs are the most recent addition in the non-coding RNA family, which has started to gain recognition after a decade of obscurity. The first couple of reports that emerged at the beginning of this decade and the amount of evidence that has accumulated thereafter has, however, encouraged RNA researchers to navigate further in the quest for the exploration of circular RNAs. The joining of 5′ and 3′ ends of RNA molecules through backsplicing forms circular RNAs during co-transcriptional or post-transcriptional processes. These molecules are capable of effectively sponging microRNAs, thereby regulating the cellular processes, as evidenced by numerous animal and plant systems. Preliminary studies have shown that circular RNA has an imperative role in transcriptional regulation and protein translation, and it also has significant therapeutic potential. The high stability of circular RNA is rendered by its closed ends; they are nevertheless prone to degradation by circulating endonucleases in serum or exosomes or by microRNA-mediated cleavage due to their high complementarity. However, the identification of circular RNAs involves diverse methodologies and the delineation of its possible role and mechanism in the regulation of cellular and molecular architecture has provided a new direction for the continuous research into circular RNA. In this review, we discuss the possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems.
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Affiliation(s)
- Ashirbad Guria
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Priyanka Sharma
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Sankar Natesan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
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50
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Wang M, Gu B, Yao G, Li P, Wang K. Circular RNA Expression Profiles and the Pro-tumorigenic Function of CircRNA_10156 in Hepatitis B Virus-Related Liver Cancer. Int J Med Sci 2020; 17:1351-1365. [PMID: 32624692 PMCID: PMC7330659 DOI: 10.7150/ijms.45637] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/19/2020] [Indexed: 12/18/2022] Open
Abstract
Liver cancer is one of the most common malignant tumors in the world. Circular RNAs (circRNAs) perform important functions in cancer progression and are regarded as prospective biomarkers for cancer diagnosis and therapy. Here, we used the high-throughput RNA sequencing technology in conjunction with bioinformatics tools to profile circRNA expression in patients with HBV-related liver cancer. A total of 13,124 circRNAs were identified in HBV-related liver cancer, approximately 86.25% of which were sense-overlapping circRNAs. Moreover, 2,996 circRNAs exhibited different expression patterns between liver cancer tissues and matched pericancerous tissues. Function annotation indicated that these aberrantly expressed circRNAs were primarily engaged in cellular processes and cancer-associated pathways. Notably, the circRNA-miRNA interaction networks showed that 6,020 circRNAs were predicted to target 1,654 miRNAs. Quantitative RT-PCR (qRT-PCR) assay indicated that ten randomly selected circRNAs displayed consistent expression patterns with the sequencing results. We further predicted that circRNA_10156 might work as a molecular sponge of miR-149-3p, which served an important function in tumor development. Consequently, our results demonstrated that depletion of circRNA_10156 upregulated miR-149-3p, reduced Akt1 expression, and suppressed liver cancer cell proliferation. The present study will facilitate the elucidation of biological functions of circRNAs in the progression of HBV-related liver cancer providing prospective biomarkers and therapeutic targets for this disease. Our findings also reveal that circRNA_10156 might represent a promising therapeutic target for liver cancer management.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Bianli Gu
- Henan Key Laboratory of Cancer Epigenetics, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Guoliang Yao
- Department of General Surgery, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471003, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, China
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