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Biferali B, Mocciaro E, Runfola V, Gabellini D. Long non-coding RNAs and their role in muscle regeneration. Curr Top Dev Biol 2024; 158:433-465. [PMID: 38670715 DOI: 10.1016/bs.ctdb.2024.02.010] [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: 04/28/2024]
Abstract
In mammals, most of the genome is transcribed to generate a large and heterogeneous variety of non-protein coding RNAs, that are broadly grouped according to their size. Long noncoding RNAs include a very large and versatile group of molecules. Despite only a minority of them has been functionally characterized, there is emerging evidence indicating long noncoding RNAs as important regulators of expression at multiple levels. Several of them have been shown to be modulated during myogenic differentiation, playing important roles in the regulation of skeletal muscle development, differentiation and homeostasis, and contributing to neuromuscular diseases. In this chapter, we have summarized the current knowledge about long noncoding RNAs in skeletal muscle and discussed specific examples of long noncoding RNAs (lncRNAs and circRNAs) regulating muscle stem cell biology. We have also discussed selected long noncoding RNAs involved in the most common neuromuscular diseases.
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Affiliation(s)
- Beatrice Biferali
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Mocciaro
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Runfola
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Gabellini
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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2
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Li Y, Shi R, Yuan R, Jiang Y. Comprehensive transcriptional analysis of pig facial skin development. PeerJ 2023; 11:e15955. [PMID: 37663277 PMCID: PMC10470455 DOI: 10.7717/peerj.15955] [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: 05/16/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023] Open
Abstract
Background Skin development is a complex process that is influenced by many factors. Pig skin is used as an ideal material for xenografts because it is more anatomically and physiologically similar to human skin. It has been shown that the skin development of different pig breeds is different, and some Chinese pig breeds have the characteristics of skin thickness and facial skin folds, but the specific regulatory mechanism of this skin development is not yet clear. Methods In this study, the facial skin of Chenghua sows in the four developmental stages of postnatal Day 3 (D3) , Day 90 (D90) , Day 180 (D180), and Year 3 (Y3) were used as experimental materials, and RNA sequencing (RNA-seq) analysis was used to explore the changes in RNA expression in skin development at the four developmental stages, determine the differentially expressed messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), and perform functional analysis of related genes by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results A pairwise comparison of the four developmental stages identified several differentially expressed genes (DEGs) and found that the number of differentially expressed RNAs (DE RNAs) increased with increasing developmental time intervals. Elastin (ELN) is an important component of the skin. Its content affects the relaxation of the epidermis and dermal connection, and its expression is continuously downregulated during the four developmental stages. The functions of DEGs at different developmental stages were examined by performing GO and KEGG analyses, and the GO terms and enrichment pathways of mRNAs, lncRNAs, miRNAs, and circRNAs highly overlapped, among which the PPAR signaling pathway, a classical pathway for skin development, was enriched by DEGs of D3 vs. D180, D90 vs. D180 and D180 vs. Y3. In addition, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA interaction networks and found genes that may be associated with skin development, but their interactions need further study. Conclusions We identified a number of genes associated with skin development, performed functional analyses on some important DEGs and constructed interaction networks that facilitate further studies of skin development.
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Affiliation(s)
- Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya’an, Sichuan, China
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Zhang Z, Huang Y, Guo AY, Yang L. Research progress of circular RNA molecules in aging and age-related diseases. Ageing Res Rev 2023; 87:101913. [PMID: 36934850 DOI: 10.1016/j.arr.2023.101913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/05/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-chain endogenous closed circular RNAs that do not have a poly(A) tail at the 3' end and a cap structure at the 5' end and are connected end-to-end by covalent bonds. CircRNAs, which are pervasive, diverse, stable, and conversed, have functions in transcriptional control and protein translation and play vital roles in modulating cell senescence, individual aging, as well as the occurrence and development of age-related diseases. Studies in recent years were reviewed from aspects including the biosynthesis mechanisms, classification, expression, biomedical functions, associations with aging and age-related diseases, and potential clinical applications of circRNAs. It will provide the theoretic basis for exploring the molecular biological mechanisms of aging, using circRNA as the therapeutic target to delay aging, and finding therapeutic strategies to prevent and treat age-related diseases.
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Affiliation(s)
- Zhidan Zhang
- Departments of Infectious Disease, The First Hospital of China Medical University, Shenyang, PR China
| | - Yuling Huang
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, PR China
| | - AYao Guo
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, PR China.
| | - Lina Yang
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, PR China.
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Yu X, Liu H, Chang N, Fu W, Guo Z, Wang Y. Circular RNAs: New players involved in the regulation of cognition and cognitive diseases. Front Neurosci 2023; 17:1097878. [PMID: 36816112 PMCID: PMC9932922 DOI: 10.3389/fnins.2023.1097878] [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: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Circular RNAs (circRNAs), a type of covalently closed endogenous single-stranded RNA, have been regarded as the byproducts of the aberrant splicing of genes without any biological functions. Recently, with the development of high-throughput sequencing and bioinformatics, thousands of circRNAs and their differential biological functions have been identified. Except for the great advances in identifying circRNA roles in tumor progression, diagnosis, and treatment, accumulated evidence shows that circRNAs are enriched in the brain, especially in the synapse, and dynamically change with the development or aging of organisms. Because of the specific roles of synapses in higher-order cognitive functions, circRNAs may not only participate in cognitive functions in normal physiological conditions but also lead to cognition-related diseases after abnormal regulation of their expression or location. Thus, in this review, we summarized the progress of studies looking at the role of circRNA in cognitive function, as well as their involvement in the occurrence, development, prognosis, and treatment of cognitive-related diseases, including autism, depression, and Alzheimer's diseases.
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Affiliation(s)
- Xiaohan Yu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Haoyu Liu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Chang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Weijia Fu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhiwen Guo
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yue Wang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Yue Wang,
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5
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Yu W, Yang MK, Sung DJ, Park TJ, Kim M, Ntigura E, Kim SH, Kim B, Park SW, Bae YM. Differential expression profiles of miRNA in the serum of sarcopenic rats. Biochem Biophys Rep 2022; 30:101251. [PMID: 35313645 PMCID: PMC8933690 DOI: 10.1016/j.bbrep.2022.101251] [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: 01/19/2022] [Revised: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 11/30/2022] Open
Abstract
As the geriatric population and life expectancy increase, the interest in preventing geriatric diseases, such as sarcopenia, is increasing. However, the causes of sarcopenia are unclear, and current diagnostic methods for sarcopenia are unreliable. We hypothesized that the changes in the expression of certain miRNAs may be associated with the pathophysiology of sarcopenia. Herein, we analyzed the miRNA expression profiles in the blood of young (3-months-old) healthy rats, old sarcopenic (17-months-old) rats, and age-matched (17-months-old) control rats. The changes in miRNA expression levels were analyzed using Bowtie 2 software. A total of 523 miRNAs were detected in the rat serum. Using scatter plots and clustering heatmap data, we found 130 miRNAs that were differentially expressed in sarcopenic rats (>2-fold change) compared to the expression in young healthy and age-matched control rats. With a threshold of >5-fold change, we identified 14 upregulated miRNAs, including rno-miR-133b-3p, rno-miR-133a-3p, rno-miR-133c, rno-miR-208a-3p, and rno-miR434-5p among others in the serum of sarcopenic rats. A protein network map based on these 14 miRNAs identified the genes involved in skeletal muscle differentiation, among which Notch1, Egr2, and Myocd represented major nodes. The data obtained in this study are potentially useful for the early diagnosis of sarcopenia and for the identification of novel therapeutic targets for the treatment and/or prevention of sarcopenia. Early diagnosis of sarcopenia and discovery of therapeutic targets are necessary. We determined the significantly increased miRNAs in the serum of sarcopenic rats. They include rno-miR-133b-3p, 133a-3p, 133c, 208a-3p, and miR434-5p. Network mapping from the miRNA expression profiles helps identify target proteins. Notch, Egr, and Myocd genes were suggested as targets for sarcopenia treatment.
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Affiliation(s)
- Wonjong Yu
- Department of Physical Therapy, Eulji University, South Korea
| | - Min-kyu Yang
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
| | - Dong Jun Sung
- Department of Sport and Health Studies, College of Biomedical and Health Science, Konkuk University, Chungju, Republic of Korea
| | - Tae Jun Park
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
| | - Myungchul Kim
- Department of Physical Therapy, Eulji University, South Korea
| | - Eustache Ntigura
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
- Department of Preventive and Community Dentistry, School of Dentistry, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Sung Hea Kim
- Department of Cardiology, Konkuk University School of Medicine, Seoul, South Korea
| | - Bokyung Kim
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
| | - Sang Woong Park
- Department of Emergency Medical Services, Eulji University, South Korea
- Corresponding author.
| | - Young Min Bae
- Department of Physiology, KU Open Innovation Center, Research Institute of Medical Science, Konkuk University School of Medicine, Chungju, South Korea
- Corresponding author.
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Wu Z, Fan H, Jin J, Gao S, Huang R, Wu S, Bao W. Insight into mechanisms of pig lncRNA FUT3-AS1 regulating E. coli F18-bacterial diarrhea. PLoS Pathog 2022; 18:e1010584. [PMID: 35696408 PMCID: PMC9191744 DOI: 10.1371/journal.ppat.1010584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/10/2022] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli F18 is a common conditional pathogen that is associated with a variety of infections in humans and animals. LncRNAs have emerged as critical players in pathogen infection, but their role in the resistance of the host to bacterial diarrhea remains unknown. Here, we used piglets as animal model and identified an antisense lncRNA termed FUT3-AS1 as a host regulator related to E. coli F18 infection by RNA sequencing. Downregulation of FUT3-AS1 expression contributed to the enhancement of E. coli F18 resistance in IPEC-J2 cells. FUT3-AS1 knockdown reduced FUT3 expression via decreasing the H4K16ac level of FUT3 promoter. Besides, the FUT3-AS1/miR-212 axis could act as a competing endogenous RNA to regulate FUT3 expression. Functional analysis demonstrated that target FUT3 plays a vital role in the resistance of IPEC-J2 cells to E. coli F18 invasion. A Fut3-knockout mice model was established and Fut3-knockout mice obviously improved the ability of resistance to bacterial diarrhea. Interestingly, FUT3 could enhance E. coli F18 susceptibility by activating glycosphingolipid biosynthesis and toll-like receptor signaling which are related to receptor formation and immune response, respectively. In summary, we have identified a novel biomarker FUT3-AS1 that modulates E. coli F18 susceptibility via histone H4 modifications or miR-212/FUT3 axis, which will provide theoretical guidance to develop novel strategies for combating bacterial diarrhea in piglets.
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Affiliation(s)
- Zhengchang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P. R. China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Hairui Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jian Jin
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Song Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
| | - Shenglong Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P. R. China
- * E-mail:
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7
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Gao F, Li J, Liang S, Wei L, He X, Liu S, Cheng X, Shi K, Jiang H, Chen L. Emerging roles of circRNAs in mice kidney with aging. Microsc Res Tech 2022; 85:2984-2996. [PMID: 35656876 DOI: 10.1002/jemt.24147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 11/06/2022]
Abstract
Circular RNA (circRNA) is a novel type of noncoding RNA expressed in different tissues and species. Up to now, little is known of the function and expression of circRNAs in kidney aging. In this research, we used RNA sequencing to identify 11,929 circRNAs in kidney from 3-, 12-, and 24-month-old mice, of which 12 circRNAs were validated by qPCR. Based on the validated circRNAs and their predicted miRNA-mRNA target pairs, a circRNA-miRNA-mRNA interactions network was conducted. Bioinformatics analysis for all the mRNAs in the ceRNA network showed that the most enriched gene ontology (GO) term and one of the most enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were associated with endoplasmic reticulum (ER). The network also identified circNpas2, which was decreased significantly in mice kidney during aging, as a hub gene. Subsequently, we found that the cell cycle was arrested in G1 phase and the expression of P53 and P16 increased significantly in the circNpas2-knockdown cells. Moreover, knockdown of circNpas2 inhibited expression of ER-related proteins, HSPA5 and ERO1L. Taken together, our findings contribute to a better understanding of the role played by circRNA during kidney aging and provide potential therapeutic targets for the prevention of kidney aging.
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Affiliation(s)
- Fanfan Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jie Li
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shanshan Liang
- Blood Transfusion Department, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Limin Wei
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin He
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Sixiu Liu
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Cheng
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kehui Shi
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hongli Jiang
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lei Chen
- Dialysis Department of Nephrology Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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8
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Gao X, Tian X, Huang Y, Fang R, Wang G, Li D, Zhang J, Li T, Yuan R. Role of circular RNA in myocardial ischemia and ageing-related diseases. Cytokine Growth Factor Rev 2022; 65:1-11. [PMID: 35561533 DOI: 10.1016/j.cytogfr.2022.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/10/2023]
Abstract
Circular RNA (circRNA) is a new endogenous transcription product, which has attracted significant attention in RNA biology research.CircRNA comprise exons or introns involved in regulation of various mechanisms.These molecules are stable and species-specific, as well as cell and tissue-specific.Cardiovascular diseases particularly myocardial ischemia and ageing-related diseases, pose a major health care burden and novel treatments and biomarkers should be explored.Recent findings indicate that circRNAs are implicated in biological processes, such as glucose metabolism, fatty acid oxidation, mitochondrial biosynthesis, implying that they are potential targets for myocardial ischemia treatment.In the present review, the functions of circRNAs in the heart are described, with emphasis given on in the relationship with myocardial ischemia and cardiac aging-related diseases.Directions for future research are also summarized.
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Affiliation(s)
- Xiaolong Gao
- School of Graduate, Shaanxi University of Chinese Medicine, No. 1 Middle section of Shiji Avenue, Xianyang 712046, China; Department of Cardiology, Shaanxi Provincial Hospital of Chinese Medicine, No.4 Xihuamen Street, Xi'an 710003, China
| | - Xin Tian
- Department of Cardiology, Shaanxi Provincial Hospital of Chinese Medicine, No.4 Xihuamen Street, Xi'an 710003, China
| | - Ye Huang
- Department of Emergency, Xiyuan Hospital, China Academy of Chinese Medical Sciences, No.1 Xiyuan Playground Street, Beijing 100091, China
| | - Rong Fang
- School of Graduate, Shaanxi University of Chinese Medicine, No. 1 Middle section of Shiji Avenue, Xianyang 712046, China
| | - Gendi Wang
- School of Graduate, Shaanxi University of Chinese Medicine, No. 1 Middle section of Shiji Avenue, Xianyang 712046, China; Department of Cardiology, Shaanxi Provincial Hospital of Chinese Medicine, No.4 Xihuamen Street, Xi'an 710003, China
| | - Dan Li
- School of Graduate, Shaanxi University of Chinese Medicine, No. 1 Middle section of Shiji Avenue, Xianyang 712046, China; Department of Cardiology, Shaanxi Provincial Hospital of Chinese Medicine, No.4 Xihuamen Street, Xi'an 710003, China
| | - Junru Zhang
- Department of Cardiology, Shaanxi Provincial Hospital of Chinese Medicine, No.4 Xihuamen Street, Xi'an 710003, China.
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, No. 169 Changle West Rd, Xi'an 710032, China.
| | - Ruihua Yuan
- School of Graduate, Shaanxi University of Chinese Medicine, No. 1 Middle section of Shiji Avenue, Xianyang 712046, China; Real World Clinical Research Institute, Shaanxi University of Chinese Medicine, No. 1 Middle section of Shiji Avenue, Xianyang 712046, China.
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Herman AB, Occean JR, Sen P. Epigenetic dysregulation in cardiovascular aging and disease. THE JOURNAL OF CARDIOVASCULAR AGING 2021; 1. [PMID: 34790973 PMCID: PMC8594871 DOI: 10.20517/jca.2021.16] [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] [Indexed: 12/12/2022]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality and morbidity for all sexes, racial and ethnic groups. Age, and its associated physiological and pathological consequences, exacerbate CVD incidence and progression, while modulation of biological age with interventions track with cardiovascular health. Despite the strong link between aging and CVD, surprisingly few studies have directly investigated heart failure and vascular dysfunction in aged models and subjects. Nevertheless, strong correlations have been found between heart disease, atherosclerosis, hypertension, fibrosis, and regeneration efficiency with senescent cell burden and its proinflammatory sequelae. In agreement, senotherapeutics have had success in reducing the detrimental effects in experimental models of cardiovascular aging and disease. Aside from senotherapeutics, cellular reprogramming strategies targeting epigenetic enzymes remain an unexplored yet viable option for reversing or delaying CVD. Epigenetic alterations comprising local and global changes in DNA and histone modifications, transcription factor binding, disorganization of the nuclear lamina, and misfolding of the genome are hallmarks of aging. Limited studies in the aging cardiovascular system of murine models or human patient samples have identified strong correlations between the epigenome, age, and senescence. Here, we compile the findings in published studies linking epigenetic changes to CVD and identify clear themes of epigenetic deregulation during aging. Pending direct investigation of these general mechanisms in aged tissues, this review predicts that future work will establish epigenetic rejuvenation as a potent method to delay CVD.
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Affiliation(s)
- Allison B Herman
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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10
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The emerging role of circular RNAs in cardiovascular diseases. J Physiol Biochem 2021; 77:343-353. [PMID: 33772724 DOI: 10.1007/s13105-021-00807-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/03/2021] [Indexed: 12/23/2022]
Abstract
Cardiovascular disease (CVD) is one of the vital causes of morbidity and mortality, and the number of deaths from CVD has increased worldwide. Circular RNAs (circRNAs) is a novel type of endogenous noncoding RNA, which can form covalent closed continuous rings and are highly expressed in the eukaryotic transcriptome. In recent years, research on circRNAs have been increasing and the researchers have also become cumulatively aware of the association between circRNAs and CVD. This review highlights the biogenesis and functions of circRNAs and the role in cardiovascular diseases.
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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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Zheng Y, Liu T, Li Q, Li J. Integrated analysis of long non-coding RNAs (lncRNAs) and mRNA expression profiles identifies lncRNA PRKG1-AS1 playing important roles in skeletal muscle aging. Aging (Albany NY) 2021; 13:15044-15060. [PMID: 34051073 PMCID: PMC8221296 DOI: 10.18632/aging.203067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/28/2021] [Indexed: 12/27/2022]
Abstract
This study aimed to identify long non-coding RNAs (lncRNAs) involving in the skeletal muscle aging process. Skeletal muscle samples from old and young subjects were collected for lncRNA-sequencing. Differentially expressed genes (DEGs) and DElncRNAs between young and old groups were identified and a co-expression network was built. Further, a dexamethasone-induced muscle atrophy cell model was established to characterize the function of a critical lncRNA. A total of 424 DEGs, including 271 upregulated genes and 153 downregulated genes as well as 152 DElncRNAs including 76 up-regulated and 76 down-regulated lncRNAs were obtained. Functional analysis demonstrated that the DEGs were significantly related to immune response. Coexpression network demonstrated lncRNA AC004797.1, PRKG1-AS1 and GRPC5D-AS1 were crucial lncRNAs. Their expressions were further validated by qRT-PCR in human skeletal muscle and the muscle atrophy cell model. Further in vitro analysis suggested that knock-down of PRKG1-AS1 could significantly increase cell viability and decrease cell apoptosis. qRT-PCR and western blot analyses demonstrated that knock-down of PRKG1-AS1 could increase the expression of MyoD, MyoG and Mef2c. This study demonstrated that lncRNAs of GPRC5D-AS1, AC004797.1 and PRKG1-AS1 might involve the aging-associated disease processes.
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Affiliation(s)
- Yan Zheng
- Department of Geriatrics, The First Hospital of Jilin University, Changchun 130021, Jilin, P.R. China
| | - Ting Liu
- Department of Geriatrics, The First Hospital of Jilin University, Changchun 130021, Jilin, P.R. China
| | - Qun Li
- Department of Thyroid Surgery, The First Hospital of Jilin University, Changchun 130021, Jilin, P.R. China
| | - Jie Li
- Department of Geriatrics, The First Hospital of Jilin University, Changchun 130021, Jilin, P.R. China
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13
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Liu J, Li M, Kong L, Cao M, Zhang M, Wang Y, Song C, Fang X, Chen H, Zhang C. CircARID1A regulates mouse skeletal muscle regeneration by functioning as a sponge of miR-6368. FASEB J 2021; 35:e21324. [PMID: 33421208 DOI: 10.1096/fj.202001992r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022]
Abstract
The noncoding RNAs play important role in growth and development of mammalian skeletal muscle. Recent work has shown that circRNAs are abundant in skeletal muscle tissue, with significant changes in their expression patterns during muscle development and aging. We identified a novel circRNA called circARID1A that is highly expressed in mice skeletal muscle compare to its linear transcript. Experiments shown that circARID1A significantly inhibited the process of C2C12 cell proliferation and promoted its differentiation. Interactions between circRNA and miRNA were screened by miRNA gene chip sequencing. The results indicated that circARID1A can sponge miR-6368, which was further verified by miRNA sensor and other experiments. Besides, miR-6368 is a commonly expressed miRNA that regulates the expression of several target genes including Tlr4. A mouse model of skeletal muscle injury was successfully established to explore the role of circARID1A in skeletal muscle development and regeneration in vivo. Moreover, we found the overexpression of circARID1A significantly promoted the regeneration of skeletal muscle. The results of our study suggest that circARID1A may regulate skeletal muscle cell development and regeneration by sponging miR-6368.
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Affiliation(s)
- Jia Liu
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - MengLu Li
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - LingHao Kong
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - MengWen Cao
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - MoLan Zhang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - YanHong Wang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - ChengChuang Song
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - XingTang Fang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Hong Chen
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - ChunLei Zhang
- Institute of Cellular and Molecular Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China
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14
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Zhang L, Zhang Y, Wang Y, Zhao Y, Ding H, Li P. Circular RNAs: Functions and Clinical Significance in Cardiovascular Disease. Front Cell Dev Biol 2020; 8:584051. [PMID: 33134301 PMCID: PMC7550538 DOI: 10.3389/fcell.2020.584051] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/09/2020] [Indexed: 01/01/2023] Open
Abstract
Cardiovascular disease (CVD) causes high morbidity and mortality worldwide. Accumulating research has indicated the possible roles played by circular RNAs (circRNAs) in the pathogenesis of CVD. CircRNAs are non-coding RNAs with covalently closed loop structures. CircRNAs can function by acting as miRNA sponges, RNA binding protein sponges, mRNA transcriptional regulators and templates for protein translation. The specific characteristics of circRNAs such as high stability, abundant distribution, and tissue- and developmental stage-specific expression make them potential biomarkers for the diagnosis and prognosis of CVD. In this paper, we systematically summarized the current knowledge regarding the biogenesis, biological properties and the action mechanisms of circRNAs, elucidated the roles played by circRNAs in the pathogenesis of CVD, and explored the diagnostic potential of circRNAs in CVD. With in-depth studies, an increasing number of molecular mechanisms underlying the participation of circRNAs in CVD may be elucidated, and the application of circRNAs in the clinical diagnosis and prevention of CVD may eventually be realized.
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Affiliation(s)
- Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yanfang Zhao
- Institute of Biomedical Research, School for Life Science, Shandong University of Technology, Zibo, China
| | - Han Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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15
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Lozano-Vidal N, Bink DI, Boon RA. Long noncoding RNA in cardiac aging and disease. J Mol Cell Biol 2020; 11:860-867. [PMID: 31152659 PMCID: PMC6884711 DOI: 10.1093/jmcb/mjz046] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cardiovascular diseases (CVDs) are the main cause of morbidity and mortality in Western society and present an important age-related risk. With the constant rise in life expectancy, prevalence of CVD in the population will likely increase further. New therapies, especially in the elderly, are needed to combat CVD. This review is focused on the role of long noncoding RNA (lncRNA) in CVD. RNA sequencing experiments in the past decade showed that most RNA does not code for protein, but many RNAs function as ncRNA. Here, we summarize the recent findings of lncRNA regulation in the diseased heart. The potential use of these RNAs as biomarkers of cardiac disease prediction is also discussed.
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Affiliation(s)
- Noelia Lozano-Vidal
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, the Netherlands
| | - Diewertje I Bink
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, the Netherlands
| | - Reinier A Boon
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam Universitair Medische Centra, Vrije Universiteit Amsterdam, 1081 HZ, Amsterdam, the Netherlands.,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, Berlin, Germany
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16
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Circular RNAs: Promising Molecular Biomarkers of Human Aging-Related Diseases via Functioning as an miRNA Sponge. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:215-229. [PMID: 32637451 PMCID: PMC7326721 DOI: 10.1016/j.omtm.2020.05.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Circular RNAs (circRNAs) are a new class of noncoding single-stranded RNAs that differ from linear microRNAs (miRNAs), since they form covalently closed loop structures without free 3′ poly(A) tails or 5′ caps. circRNAs are the competitive endogenous RNAs (ceRNAs) by binding to miRNA through miRNA response elements (MREs) (i.e., “miRNA sponge”), thereby reducing the quantity of miRNA available to target mRNA, subsequently promoting mRNA stability or protein expression, which involves the initiation and progress of human diseases. Owing to these features of abundance, stability, conservative property, and tissue and stage specificity, widely distributing in the extracellular space and in various bodily fluids, circRNAs can be considered as potential biomarkers for various diseases. Here, we reviewed the promising circRNAs being disease biomarkers, focused on their regulatory function by acting as miRNA sponges, and described their roles in cancer, cardiovascular or neurodegenerative diseases, osteoarthritis, rheumatoid arthritis, diabetes, and other human aging-related diseases, which provide a new direction for pathogenesis, diagnosis, and treatment of human aging-related diseases.
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17
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Hoffman JM, Valencak TG. A short life on the farm: aging and longevity in agricultural, large-bodied mammals. GeroScience 2020; 42:909-922. [PMID: 32361879 PMCID: PMC7286991 DOI: 10.1007/s11357-020-00190-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022] Open
Abstract
As average human lifespans increase across the globe, companion animals, specifically dogs and cats, are also living longer with more age-related morbidities. However, a similar trend is not seen in mammalian livestock species. Cows, pigs, goats, and sheep, as well as more niche mammalian species raised across the world, have been primarily raised for their economic benefit to humans and are culled from the population once their production declines. To this end, we lack clear knowledge about the age-related morbidities and causes of death that afflict livestock animals due to natural aging, as well as detailed age-specific survival rates. Here, we review the current state of the field of agricultural mammal aging, as well as provide specific questions and directions that may provide novel resources for veterinarians and aging biologists. By raising awareness of the overall quality of life and ongoing health of individual livestock animals, we can potentially increase production into older life stages, leading to decreased costs to farmers and improved welfare for the animals themselves.
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Affiliation(s)
- Jessica M. Hoffman
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd.,CH464, Birmingham, AL 35294 USA
| | - Teresa G. Valencak
- College of Animal Sciences, Zhejiang University, Zijingang Campus, 866 Yuhangtang Road, Hangzhou, 310058 People’s Republic of China
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18
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Ruiz-Meana M, Bou-Teen D, Ferdinandy P, Gyongyosi M, Pesce M, Perrino C, Schulz R, Sluijter JPG, Tocchetti CG, Thum T, Madonna R. Cardiomyocyte ageing and cardioprotection: consensus document from the ESC working groups cell biology of the heart and myocardial function. Cardiovasc Res 2020; 116:1835-1849. [DOI: 10.1093/cvr/cvaa132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/25/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Abstract
Advanced age is a major predisposing risk factor for the incidence of coronary syndromes and comorbid conditions which impact the heart response to cardioprotective interventions. Advanced age also significantly increases the risk of developing post-ischaemic adverse remodelling and heart failure after ischaemia/reperfusion (IR) injury. Some of the signalling pathways become defective or attenuated during ageing, whereas others with well-known detrimental consequences, such as glycoxidation or proinflammatory pathways, are exacerbated. The causative mechanisms responsible for all these changes are yet to be elucidated and are a matter of active research. Here, we review the current knowledge about the pathophysiology of cardiac ageing that eventually impacts on the increased susceptibility of cells to IR injury and can affect the efficiency of cardioprotective strategies.
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Affiliation(s)
- Marisol Ruiz-Meana
- Department of Cardiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Universitat Autonoma de Barcelona and Centro de Investigación Biomédica en Red-CV, CIBER-CV, Madrid, Spain
| | - Diana Bou-Teen
- Department of Cardiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Universitat Autonoma de Barcelona and Centro de Investigación Biomédica en Red-CV, CIBER-CV, Madrid, Spain
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Mariann Gyongyosi
- Department of Cardiology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Maurizio Pesce
- Unità di Ingegneria Tissutale Cardiovascolare, Centro Cardiologico Monzino, IRCCS, Milan, Italy
| | - Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Rainer Schulz
- Institute of Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Joost P G Sluijter
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
- Circulatory Health Laboratory, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Carlo G Tocchetti
- Department of Translational Medical Sciences and Interdepartmental Center of Clinical and Translational Sciences (CIRCET), Federico II University, Naples, Italy
| | - Thomas Thum
- Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Rosalinda Madonna
- Institute of Cardiology, University of Pisa, Pisa, Italy
- Department of Internal Medicine, University of Texas Medical School in Houston, Houston, TX, USA
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19
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Chen Z, Pan X, Kong Y, Jiang Y, Zhong Y, Zhang H, Zhang Z, Yuan X, Li J. Pituitary-Derived Circular RNAs Expression and Regulatory Network Prediction During the Onset of Puberty in Landrace × Yorkshire Crossbred Pigs. Front Genet 2020; 11:135. [PMID: 32180798 PMCID: PMC7059797 DOI: 10.3389/fgene.2020.00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/04/2020] [Indexed: 01/25/2023] Open
Abstract
Being the center of the hypothalamus-pituitary-ovary (HPO) axis, the pituitary plays a key role in the onset of puberty. Recent studies show that circular RNAs (circRNAs) can perform as miRNA sponges to regulate development in animals. However, the function of pituitary-derived circRNAs in first estrus remains unclear in pigs. In this study, we performed a genome-wide identification and characterization of circRNAs using pituitaries from Landrace × Yorkshire crossbred pigs at three stages: pre-, in-, and post-puberty, to describe such pituitary-derived circRNAs in pigs. A total of 5148 circRNAs were found in the gilts' pituitaries, averaging 18 682 bp in genomic distance, which consisted of approximately 91% exonic, 6% intergenic, and 3% intronic circRNAs. Furthermore, 158 novel circRNAs were identified for the first time and classified as putative pituitary-specific circRNAs. Their expression levels during the onset of puberty, significantly exceeded those of the other circRNAs, and the parental genes of these putative pituitary-specific circRNAs were enriched in "ssc04917: prolactin signaling pathway," "ssc04080: neuroactive ligand-receptor interaction," and "ssc04728: dopaminergic synapse" pathways, all of which were consistent with pituitary functioning. Additionally, 17 differentially regulated circRNAs were found and investigated for their potential interaction with miRNAs, along with genes, by constructing a circRNA-targeted miRNA-gene network. Taken together, these results provide new insight into the circRNA-mediated timing of puberty in gilts at the pituitary level.
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Affiliation(s)
- Zitao Chen
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiangchun Pan
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yaru Kong
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yao Jiang
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yuyi Zhong
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Hao Zhang
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhe Zhang
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaolong Yuan
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaqi Li
- National Engineering Research Centre for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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20
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Dalton S, Smith K, Singh K, Kaiser H, Kolhe R, Mondal AK, Khayrullin A, Isales CM, Hamrick MW, Hill WD, Fulzele S. Accumulation of kynurenine elevates oxidative stress and alters microRNA profile in human bone marrow stromal cells. Exp Gerontol 2020; 130:110800. [PMID: 31790802 PMCID: PMC6998036 DOI: 10.1016/j.exger.2019.110800] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 02/09/2023]
Abstract
Kynurenine, a metabolite of tryptophan breakdown, has been shown to increase with age, and plays a vital role in a number of age-related pathophysiological changes, including bone loss. Accumulation of kynurenine in bone marrow stromal cells (BMSCs) has been associated with a decrease in cell proliferation and differentiation, though the exact mechanism by which kynurenine mediates these changes is poorly understood. MiRNAs have been shown to regulate BMSC function, and accumulation of kynurenine may alter the miRNA expression profile of BMSCs. The aim of this study was to identify differentially expressed miRNAs in human BMSCs in response to treatment with kynurenine, and correlate miRNAs function in BMSCs biology through bioinformatics analysis. Human BMSCs were cultured and treated with and without kynurenine, and subsequent miRNA isolation was performed. MiRNA array was performed to identify differentially expressed miRNA. Microarray analysis identified 50 up-regulated, and 36 down-regulated miRNAs in kynurenine-treated BMSC cultures. Differentially expressed miRNA included miR-1281, miR-330-3p, let-7f-5p, and miR-493-5p, which are important for BMSC proliferation and differentiation. KEGG analysis found up-regulated miRNA targeting glutathione metabolism, a pathway critical for removing oxidative species. Our data support that the kynurenine dependent degenerative effect is partially due to changes in the miRNA profile of BMSCs.
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Affiliation(s)
- Sherwood Dalton
- Department of Orthopedics, Augusta University, Augusta, GA, United States of America
| | - Kathryn Smith
- Department of Orthopedics, Augusta University, Augusta, GA, United States of America
| | - Kanwar Singh
- Department of Orthopedics, Augusta University, Augusta, GA, United States of America
| | - Helen Kaiser
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, United States of America
| | - Ravindra Kolhe
- Departments of Pathology, Augusta University, Augusta, GA 30912, United States of America
| | - Ashis K Mondal
- Departments of Pathology, Augusta University, Augusta, GA 30912, United States of America
| | - Andrew Khayrullin
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, United States of America
| | - Carlos M Isales
- Department of Orthopedics, Augusta University, Augusta, GA, United States of America; Department of Medicine, Augusta University, Augusta, GA, United States of America; Institute of Healthy Aging, Augusta University, Augusta, GA, United States of America
| | - Mark W Hamrick
- Department of Orthopedics, Augusta University, Augusta, GA, United States of America; Department of Cell biology and Anatomy, Augusta University, Augusta, GA, United States of America; Institute of Healthy Aging, Augusta University, Augusta, GA, United States of America
| | - William D Hill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29403, United States of America; Ralph H Johnson Veterans Affairs Medical Center, Charleston, SC, 29403, United States of America
| | - Sadanand Fulzele
- Department of Orthopedics, Augusta University, Augusta, GA, United States of America; Department of Cell biology and Anatomy, Augusta University, Augusta, GA, United States of America; Institute of Healthy Aging, Augusta University, Augusta, GA, United States of America.
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21
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Cai H, Li Y, Li H, Niringiyumukiza JD, Zhang M, Chen L, Chen G, Xiang W. Identification and characterization of human ovary-derived circular RNAs and their potential roles in ovarian aging. Aging (Albany NY) 2019; 10:2511-2534. [PMID: 30260796 PMCID: PMC6188495 DOI: 10.18632/aging.101565] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/14/2018] [Indexed: 12/21/2022]
Abstract
Circular RNAs (circRNAs) have recently been shown to exert effects on multiple pathological processes by acting as miRNA sponges. However, the roles of circRNAs in ovarian senescence are largely unknown. The objective of this study was to identify the circRNAs involved in ovarian aging and predict their potential biological functions. We first performed RNA-sequencing to generate ovarian circRNA expression profiles from young (n = 3) and aging (n = 3) groups. In total, 48,220 circRNAs were identified, of which 194 circRNAs were significantly up-regulated and 207 circRNAs were down-regulated during aging (fold change > 2, P < 0.05). Bioinformatics analysis demonstrated that the metabolic process, regulated secretory pathway, oxidation-reduction process, steroid hormone biosynthesis, and insulin secretion pathways, which may be associated with ovarian aging, were significantly enriched (P < 0.05). The biological characteristics of ovary-derived circRNA, such as back-splicing, RNase R resistance, stability, and alternative splicing, were further validated. Bioinformatics predicted that most of the circRNAs harboured miRNA binding sites, of which circDDX10-miR-1301-3p/miR-4660-SIRT3 axis may be involved in the regulation of ovarian function. Our study indicates that circRNAs are aberrantly expressed in the aging ovary and may play potential roles in the development of ovarian senescence.
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Affiliation(s)
- Hongcai Cai
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yamin Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Huimin Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jean Damascene Niringiyumukiza
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Mengdi Zhang
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Chen
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Wenpei Xiang
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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22
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Bonnet S, Boucherat O, Paulin R, Wu D, Hindmarch CCT, Archer SL, Song R, Moore JB, Provencher S, Zhang L, Uchida S. Clinical value of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases. Am J Physiol Cell Physiol 2019; 318:C1-C28. [PMID: 31483703 DOI: 10.1152/ajpcell.00078.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although a majority of the mammalian genome is transcribed to RNA, mounting evidence indicates that only a minor proportion of these transcriptional products are actually translated into proteins. Since the discovery of the first non-coding RNA (ncRNA) in the 1980s, the field has gone on to recognize ncRNAs as important molecular regulators of RNA activity and protein function, knowledge of which has stimulated the expansion of a scientific field that quests to understand the role of ncRNAs in cellular physiology, tissue homeostasis, and human disease. Although our knowledge of these molecules has significantly improved over the years, we have limited understanding of their precise functions, protein interacting partners, and tissue-specific activities. Adding to this complexity, it remains unknown exactly how many ncRNAs there are in existence. The increased use of high-throughput transcriptomics techniques has rapidly expanded the list of ncRNAs, which now includes classical ncRNAs (e.g., ribosomal RNAs and transfer RNAs), microRNAs, and long ncRNAs. In addition, splicing by-products of protein-coding genes and ncRNAs, so-called circular RNAs, are now being investigated. Because there is substantial heterogeneity in the functions of ncRNAs, we have summarized the present state of knowledge regarding the functions of ncRNAs in heart, lungs, and skeletal muscle. This review highlights the pathophysiologic relevance of these ncRNAs in the context of human cardiovascular, pulmonary, and muscle diseases.
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Affiliation(s)
- Sébastien Bonnet
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Olivier Boucherat
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Roxane Paulin
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Danchen Wu
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Charles C T Hindmarch
- Queen's Cardiopulmonary Unit, Translational Institute of Medicine, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Stephen L Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Rui Song
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Joseph B Moore
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Steeve Provencher
- Pulmonary Hypertension and Vascular Biology Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California
| | - Shizuka Uchida
- Diabetes and Obesity Center, University of Louisville, Louisville, Kentucky.,The Christina Lee Brown Envirome Institute, Department of Medicine, University of Louisville, Louisville, Kentucky.,Cardiovascular Innovation Institute, University of Louisville, Louisville, Kentucky
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23
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Circular RNA circ-FoxO3 Inhibits Myoblast Cells Differentiation. Cells 2019; 8:cells8060616. [PMID: 31248210 PMCID: PMC6627427 DOI: 10.3390/cells8060616] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023] Open
Abstract
CircRNA is a type of closed circular non-coding RNA formed by reverse splicing and plays an important role in regulating the growth and development of plants and animals. To investigate the function of circ-FoxO3 in mouse myoblast cells' (C2C12) differentiation and proliferation, we used RT-qPCR to detect the expression level of circ-FoxO3 in mouse myoblast cells at different densities and different differentiation stages, and the specific interference fragment was used to inhibit the expression level of circ-FoxO3 in myoblast cells to observe its effect on myoblast cells proliferation and differentiation. We found that the expression level of circ-FoxO3 in myoblast cells increased with the prolongation of myoblast cells differentiation time, and its expression level decreased with the proliferation of myoblast cells. At the same time, we found that the differentiation ability of the cells was significantly increased (p < 0.05), but the cell proliferation was unchanged (p > 0.05) after inhibiting the expression of circ-FoxO3 in myoblast cells. Combining the results of bioinformatics analysis and the dual luciferase reporter experiment, we found that circ-FoxO3 is a sponge of miR-138-5p, which regulates muscle differentiation. Our study shows that circ-FoxO3 can inhibit the differentiation of C2C12 myoblast cells and lay a scientific foundation for further study of skeletal muscle development at circRNA levels.
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Chen J, Zou Q, Lv D, Raza MA, Wang X, Chen Y, Xi X, Li P, Wen A, Zhu L, Tang G, Li M, Li X, Jiang Y. Comprehensive transcriptional profiling of aging porcine liver. PeerJ 2019; 7:e6949. [PMID: 31149403 PMCID: PMC6526898 DOI: 10.7717/peerj.6949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/09/2019] [Indexed: 01/04/2023] Open
Abstract
Background Aging is a major risk factor for the development of many diseases, and the liver, as the most important metabolic organ, is significantly affected by aging. It has been shown that the liver weight tends to increase in rodents and decrease in humans with age. Pigs have a genomic structure, with physiological as well as biochemical features that are similar to those of humans, and have therefore been used as a valuable model for studying human diseases. The molecular mechanisms of the liver aging of large mammals on a comprehensive transcriptional level remain poorly understood. The pig is an ideal model animal to clearly and fully understand the molecular mechanism underlying human liver aging. Methods In this study, four healthy female Yana pigs (an indigenous Chinese breed) were investigated: two young sows (180-days-old) and two old sows (8-years-old). High throughput RNA sequencing was performed to evaluate the expression profiles of messenger RNA, long non-coding RNAs, micro RNAs, and circular RNAs during the porcine liver aging process. Gene Ontology (GO) analysis was performed to investigate the biological functions of age-related genes. Results A number of age-related genes were identified in the porcine liver. GO annotation showed that up-regulated genes were mainly related to immune response, while the down-regulated genes were mainly related to metabolism. Moreover, several lncRNAs and their target genes were also found to be differentially expressed during liver aging. In addition, the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks were assessed during liver aging. Conclusions Numerous age-related genes were identified and circRNA-miRNA co-expression networks that are active during porcine liver aging were constructed. These findings contribute to the understanding of the transcriptional foundations of liver aging and also provide further references that clarify human liver aging at the molecular level.
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Affiliation(s)
- Jianning Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Daojun Lv
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd, Chengdu, Sichuan, China
| | - Muhammad Ali Raza
- Department of Crop Cultivation and Farming System, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xue Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yan Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Xiaoyu Xi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Peilin Li
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd, Chengdu, Sichuan, China
| | - Anxiang Wen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
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Wang W, Wang Y, Piao H, Li B, Huang M, Zhu Z, Li D, Wang T, Xu R, Liu K. Circular RNAs as potential biomarkers and therapeutics for cardiovascular disease. PeerJ 2019; 7:e6831. [PMID: 31119072 PMCID: PMC6511224 DOI: 10.7717/peerj.6831] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/21/2019] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are genetic regulators that were earlier considered as "junk". In contrast to linear RNAs, they have covalently linked ends with no polyadenylated tails. CircRNAs can act as RNA-binding proteins, sequestering agents, transcriptional regulators, as well as microRNA sponges. In addition, it is reported that some selected circRNAs are transformed into functional proteins. These RNA molecules always circularize through covalent bonds, and their presence has been demonstrated across species. They are usually abundant and stable as well as evolutionarily conserved in tissues (liver, lung, stomach), saliva, exosomes, and blood. Therefore, they have been proposed as the "next big thing" in molecular biomarkers for several diseases, particularly in cancer. Recently, circRNAs have been investigated in cardiovascular diseases (CVD) and reported to play important roles in heart failure, coronary artery disease, and myocardial infarction. Here, we review the recent literature and discuss the impact and the diagnostic and prognostic values of circRNAs in CVD.
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Affiliation(s)
- Weitie Wang
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Yong Wang
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Hulin Piao
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Bo Li
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Maoxun Huang
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Zhicheng Zhu
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Dan Li
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Tiance Wang
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Rihao Xu
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
| | - Kexiang Liu
- Department of Cardiovascular Surgery, The Second Hospital of Jilin University, Jilin, China
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Artemenkov AA. Disadaptive Disorders of Regulation of Functions with Aging. ADVANCES IN GERONTOLOGY 2019. [DOI: 10.1134/s2079057019020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Moskalev A, Guvatova Z, Shaposhnikov M, Lashmanova E, Proshkina E, Koval L, Zhavoronkov A, Krasnov G, Kudryavtseva A. The Neuronal Overexpression of Gclc in Drosophila melanogaster Induces Life Extension With Longevity-Associated Transcriptomic Changes in the Thorax. Front Genet 2019; 10:149. [PMID: 30891062 PMCID: PMC6411687 DOI: 10.3389/fgene.2019.00149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/12/2019] [Indexed: 01/24/2023] Open
Abstract
Some effects of aging in animals are tissue-specific. In D. melanogaster neuronal overexpression of Gclc increases lifespan and improves certain physiological parameters associated with health benefits such as locomotor activity, circadian rhythmicity, and stress resistance. Our previous transcriptomic analyses of Drosophila heads, primarily composed of neuronal tissue, revealed significant changes in expression levels of genes involved in aging-related signaling pathways (Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta), translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity, and transmission. Considering that various tissues age differently and age-related gene expression changes are tissue-specific, we investigated the effects of neuronal Gclc overexpression on gene expression levels in the imago thorax, which is primarily composed of muscles. A total of 58 genes were found to be differentially expressed between thoraces of control and Gclc overexpressing flies. The Gclc level demonstrated associations with expression of genes involved in the circadian rhythmicity, the genes in categories related to the muscle system process and the downregulation of genes involved in proteolysis. Most of the functional categories altered by Gclc overexpression related to metabolism including Drug metabolism, Metabolism of xenobiotics by cytochrome P450, Glutathione metabolism, Starch and sucrose metabolism, Citrate cycle (TCA cycle), One carbon pool by folate. Thus, the transcriptomic changes caused by neuron-specific Gclc overexpression in the thorax were less pronounced than in the head and affected pathways also differed from previous results. Although these pathways don't belong to the canonical longevity pathways, we suggest that they could participate in the delay of aging of Gclc overexpressing flies.
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Affiliation(s)
- Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Ekaterina Lashmanova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina Proshkina
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Liubov Koval
- Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | | | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Cai H, Li Y, Niringiyumukiza JD, Su P, Xiang W. Circular RNA involvement in aging: An emerging player with great potential. Mech Ageing Dev 2019; 178:16-24. [DOI: 10.1016/j.mad.2018.11.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/25/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
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Circular RNA circHIPK3 Promotes the Proliferation and Differentiation of Chicken Myoblast Cells by Sponging miR-30a-3p. Cells 2019; 8:cells8020177. [PMID: 30791438 PMCID: PMC6406597 DOI: 10.3390/cells8020177] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/15/2019] [Accepted: 02/17/2019] [Indexed: 12/26/2022] Open
Abstract
Circular RNAs and microRNAs widely exist in various species and play crucial roles in multiple biological processes. It is essential to study their roles in myogenesis. In our previous sequencing data, both miR-30a-3p and circular HIPK3 (circHIPK3) RNA, which are produced by the third exon of the HIPK3 gene, were differentially expressed among chicken skeletal muscles at 11 embryo age (E11), 16 embryo age (E16), and 1-day post-hatch (P1). Here, we investigated their potential roles in myogenesis. Proliferation experiment showed that miR-30a-3p could inhibit the proliferation of myoblast. Through dual-luciferase assay and Myosin heavy chain (MYHC) immunofluorescence, we found that miR-30a-3p could inhibit the differentiation of myoblast by binding to Myocyte Enhancer Factor 2 C (MEF2C), which could promote the differentiation of myoblast. Then, we found that circHIPK3 could act as a sponge of miR-30a-3p and exerted a counteractive effect of miR-30a-3p by promoting the proliferation and differentiation of myoblasts. Taking together, our data suggested that circHIPK3 could promote the chicken embryonic skeletal muscle development by sponging miR-30a-3p.
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Chen J, Zou Q, Lv D, Raza MA, Wang X, Li P, Chen Y, Xi X, Wen A, Zhu L, Tang G, Li M, Li X, Jiang Y. Comprehensive transcriptional profiling of porcine brain aging. Gene 2019; 693:1-9. [PMID: 30695714 DOI: 10.1016/j.gene.2019.01.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/27/2018] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
Abstract
The brain as an important organ can be affected largely by aging, and the comprehensive transcriptional underpinnings of brain aging remain poorly understood. Here, we performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and circular RNAs (circRNAs) in porcine brain. We have identified 714 mRNAs, 38lncRNAs, 41miRNAs, and 148circRNAs were age-related genes in the porcine cerebral cortex. The lncRNAs, miRNAs and circRNAs have effect on the age of porcine brain due to the much changes of expression level as noncoding RNAs. The up-regulated genes were significantly enriched for stress response, reproductive regulatory process, immune response and metabolic process, and the down-regulated genes were related to neurologic function, stress response and signaling pathway. The synaptic transmission pathway may be the key role in aging of porcine brain that it was co-enriched for in both differentially expressed mRNAs and lncRNAs. Moreover, some lncRNAs and their target genes were also differentially expressed during brain aging. We further assessed the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks during brain aging. We also selected 2 mRNAs, 2 lncRNAs, 2 miRNAs, and 1 circRNAs to perform the q-PCR, and the expression patterns were highly consistent between the two methods confirming the high reproducibility and reliability of the gene expression profiling in our study. In conclusion, our findings will contribute to understand the transcriptional underpinnings of brain aging and provide a foundation for future studies on the molecular mechanisms underlying brain aging.
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Affiliation(s)
- Jianning Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Daojun Lv
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd., Chengdu, Sichuan 611130, China
| | - Muhammad Ali Raza
- Department of Crop Cultivation and Farming System, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xue Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Peilin Li
- Sichuan Weimu Modern Agricultural Science and Technology Co., Ltd., Chengdu, Sichuan 611130, China
| | - Yan Chen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiaoyu Xi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Anxiang Wen
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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Greco S, Cardinali B, Falcone G, Martelli F. Circular RNAs in Muscle Function and Disease. Int J Mol Sci 2018; 19:ijms19113454. [PMID: 30400273 PMCID: PMC6274904 DOI: 10.3390/ijms19113454] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of RNA produced during pre-mRNA splicing that are emerging as new members of the gene regulatory network. In addition to being spliced in a linear fashion, exons of pre-mRNAs can be circularized by use of the 3' acceptor splice site of upstream exons, leading to the formation of circular RNA species. In this way, genetic information can be re-organized, increasing gene expression potential. Expression of circRNAs is developmentally regulated, tissue and cell-type specific, and shared across eukaryotes. The importance of circRNAs in gene regulation is now beginning to be recognized and some putative functions have been assigned to them, such as the sequestration of microRNAs or proteins, the modulation of transcription, the interference with splicing, and translation of small proteins. In accordance with an important role in normal cell biology, circRNA deregulation has been reported to be associated with diseases. Recent evidence demonstrated that circRNAs are highly expressed in striated muscle tissue, both skeletal and cardiac, that is also one of the body tissue showing the highest levels of alternative splicing. Moreover, initial studies revealed altered circRNA expression in diseases involving striated muscle, suggesting important functions of these molecules in the pathogenetic mechanisms of both heart and skeletal muscle diseases. The recent findings in this field will be described and discussed.
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Affiliation(s)
- Simona Greco
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
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