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Wang H, Liu M, Tang H, Zhang Z, Wen H, He F. Identification and functional analysis of circpdlim5a generated from pdlim5a gene splicing in the skeletal muscle of Japanese flounder (Paralichthys olivaceus). Gen Comp Endocrinol 2024; 352:114500. [PMID: 38508470 DOI: 10.1016/j.ygcen.2024.114500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Circular RNAs (circRNAs) are non-coding RNAs with endogenous regulatory functions, including regulating skeletal muscle development. However, its role in the development of skeletal muscle in Japanese flounder (Paralichthys olivaceus) is not clear. Therefore we screened a candidate circpdlim5a, which is derived from the gene pdlim5a, from the skeletal muscle transcriptome of Japanese flounder. We characterized circpdlim5a, which was more stable compared to the linear RNA pdlim5a. Distributional characterization of circpdlim5a showed that circpdlim5a was predominantly distributed in the nucleus and was highly expressed in the skeletal muscle of adult Japanese flounder (24 months). When we further studied the circpdlim5a function, we found that it inhibited the expression of proliferation and differentiation genes according to the over-expression experiment of circpdlim5a in myoblasts. We concluded that circpdlim5a may inhibit the proliferation and differentiation of myoblasts and thereby inhibit skeletal muscle development in Japanese flounder. This experiment provides information for the study of circRNAs by identifying circpdlim5a and exploring its function, and offers clues for molecular breeding from an epigenetic perspective.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Min Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Hengtai Tang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Zhirui Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266000, China.
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Zhang Y, Wang H, Li X, Yang C, Yu C, Cui Z, Liu A, Wang Q, Liu L. Genome-wide characteristics and potential functions of circular RNAs from the embryo muscle development in Chengkou mountain chicken. Front Vet Sci 2024; 11:1375042. [PMID: 38872802 PMCID: PMC11171140 DOI: 10.3389/fvets.2024.1375042] [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: 01/24/2024] [Accepted: 04/29/2024] [Indexed: 06/15/2024] Open
Abstract
The Chengkou mountain chicken, a native Chinese poultry breed, holds significant importance in the country's poultry sector due to its delectable meat and robust stress tolerance. Muscle growth and development are pivotal characteristics in poultry breeding, with muscle fiber development during the embryonic period crucial for determining inherent muscle growth potential. Extensive evidence indicates that non-coding RNAs (ncRNAs) play a regulatory role in muscle growth and development. Among ncRNAs, circular RNAs (circRNAs), characterized by a closed-loop structure, have been shown to modulate biological processes through the regulation of microRNAs (miRNAs). This study seeks to identify and characterize the spatiotemporal-specific expression of circRNAs during embryonic muscle development in Chengkou mountain chicken, and to construct the potential regulatory network of circRNAs-miRNA-mRNAs. The muscle fibers of HE-stained sections became more distinct, and their boundaries were more defined over time. Subsequent RNA sequencing of 12 samples from four periods generated 9,904 novel circRNAs, including 917 differentially expressed circRNAs. The weighted gene co-expression network analysis (WGCNA)-identified circRNA source genes significantly enriched pathways related to cell fraction, cell growth, and muscle fiber growth regulation. Furthermore, a competitive endogenous RNA (ceRNA) network constructed using combined data of present and previous differentially expressed circRNAs, miRNA, and mRNA revealed that several circRNA transcripts regulate MYH1D, MYH1B, CAPZA1, and PERM1 proteins. These findings provide insight into the potential pathways and mechanisms through which circRNAs regulate embryonic muscle development in poultry, a theoretical support for trait improvement in domestic chickens.
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Affiliation(s)
- Yang Zhang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Haiwei Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Xingqi Li
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Chaowu Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Chunlin Yu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zhifu Cui
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Anfang Liu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qigui Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Chongqing, China
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Gu X, Yu J, Jiao K, Deng J, Xia X, Qiao K, Yue D, Gao M, Zhao C, Dong J, Huang G, Shan J, Yan C, Di L, Da Y, Zhu W, Xi J, Wang Z. Non-coding CGG repeat expansion in LOC642361/NUTM2B-AS1 is associated with a phenotype of oculopharyngodistal myopathy. J Med Genet 2024; 61:340-346. [PMID: 37923380 DOI: 10.1136/jmg-2023-109345] [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: 04/20/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Oculopharyngodistal myopathy (OPDM) is a rare adult-onset neuromuscular disease, associated with CGG repeat expansions in the 5' untranslated region of LRP12, GIPC1, NOTCH2NLC and RILPL1. However, the genetic cause of a proportion of pathoclinically confirmed cases remains unknown. METHODS A total of 26 OPDM patients with unknown genetic cause(s) from 4 tertiary referral hospitals were included in this study. Clinical data and laboratory findings were collected. Muscle samples were observed by histological and immunofluorescent staining. Long-read sequencing was initially conducted in six patients with OPDM. Repeat-primed PCR was used to screen the CGG repeat expansions in LOC642361/NUTM2B-AS1 in all 26 patients. RESULTS We identified CGG repeat expansion in the non-coding transcripts of LOC642361/NUTM2B-AS1 in another two unrelated Chinese cases with typical pathoclinical features of OPDM. The repeat expansion was more than 70 times in the patients but less than 40 times in the normal controls. Both patients showed no leucoencephalopathy but one showed mild cognitive impairment detected by Montreal Cognitive Assessment. Rimmed vacuoles and p62-positive intranuclear inclusions (INIs) were identified in muscle pathology, and colocalisation of CGG RNA foci with p62 was also found in the INIs of patient-derived fibroblasts. CONCLUSIONS We identified another two unrelated cases with CGG repeat expansion in the long non-coding RNA of the LOC642361/NUTM2B-AS1 gene, presenting with a phenotype of OPDM. Our cases broadened the recognised phenotypic spectrum and pathogenesis in the disease associated with CGG repeat expansion in LOC642361/NUTM2B-AS1.
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Affiliation(s)
- Xinyu Gu
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiaxi Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Kexin Jiao
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Xingyu Xia
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Kai Qiao
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Dongyue Yue
- Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, China
| | - Mingshi Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Jihong Dong
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Gongchun Huang
- Department of Neurology, the First People's Hospital of Pinghu, Pinghu, Zhejiang, China
| | - Jingli Shan
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Chuanzhu Yan
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Li Di
- Department of Neurology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Yuwei Da
- Department of Neurology, Xuanwu Hospital Capital Medical University, Beijing, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Rare Disease Center, National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
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Xu J, Wen Y, Li X, Peng W, Zhang Z, Liu X, Yang P, Chen N, Lei C, Zhang J, Wang E, Chen H, Huang Y. Bovine enhancer-regulated circSGCB acts as a ceRNA to regulate skeletal muscle development via enhancing KLF3 expression. Int J Biol Macromol 2024; 261:129779. [PMID: 38290628 DOI: 10.1016/j.ijbiomac.2024.129779] [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: 11/16/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
Skeletal muscle growth and development in livestock and poultry play a pivotal role in determining the quality and yield of meat production. However, the mechanisms of myogenesis are remained unclear due to it finely regulated by a complex network of biological macromolecules. In this study, leveraging previous sequencing data, we investigated a differentially expressed circular RNA (circSGCB) present in fetal and adult muscle tissues among various ruminant species, including cattle, goat, and sheep. Our analysis revealed that circSGCB is a single exon circRNA, potentially regulated by an adjacent bovine enhancer. Functional analysis through loss-of-function tests demonstrated that circSGCB exerts inhibitory effects on bovine myoblast proliferation while promoting myocytes generation. Furthermore, we discovered that circSGCB primarily localizes to the cytoplasm, where it functions as a molecular sponge by binding to bta-miR-27a-3p. This interaction releases the mRNAs of KLF3 gene and further activates downstream functional pathways. In vivo, studies provided evidence that up-regulation of KLF3 contributes to muscle regeneration. These findings collectively suggest that circSGCB operates via a competing endogenous RNA (ceRNA) mechanism to regulate KLF3, thereby influencing myogenesis in ruminants and highlights it may as potential molecular targets for enhancing meat production in livestock and poultry industries.
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Affiliation(s)
- Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Peng
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, China
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jun Zhang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Huang K, Li Z, Zhong D, Yang Y, Yan X, Feng T, Wang X, Zhang L, Shen X, Chen M, Luo X, Cui K, Huang J, Rehman SU, Jiang Y, Shi D, Pauciullo A, Tang X, Liu Q, Li H. A Circular RNA Generated from Nebulin (NEB) Gene Splicing Promotes Skeletal Muscle Myogenesis in Cattle as Detected by a Multi-Omics Approach. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2300702. [PMID: 38036415 PMCID: PMC10797441 DOI: 10.1002/advs.202300702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/16/2023] [Indexed: 12/02/2023]
Abstract
Cattle and the draught force provided by its skeletal muscle have been integral to agro-ecosystems of agricultural civilization for millennia. However, relatively little is known about the cattle muscle functional genomics (including protein coding genes, non-coding RNA, etc.). Circular RNAs (circRNAs), as a new class of non-coding RNAs, can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cattle muscle physiology function. Here, RNA-seq, Ribosome profiling (Ribo-seq), and peptidome data are integrated from cattle skeletal muscle, and detected five encoded peptides from circRNAs. It is further identified and functionally characterize a 907-amino acids muscle-specific peptide that is named circNEB-peptide because derived by the splicing of Nebulin (NEB) gene. This peptide localizes to the nucleus and cytoplasm and directly interacts with SKP1 and TPM1, key factors regulating physiological activities of myoblasts, via ubiquitination and myoblast fusion, respectively. The circNEB-peptide is found to promote myoblasts proliferation and differentiation in vitro, and induce muscle regeneration in vivo. These findings suggest circNEB-peptide is an important regulator of skeletal muscle regeneration and underscore the possibility that more encoding polypeptides derived by RNAs currently annotated as non-coding exist.
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Affiliation(s)
- Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
- School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhou510641China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Dandan Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Yufeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Liyin Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xinyue Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliasco (TO)10095Italy
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition and Feeding,Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing100193China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and EngineeringFoshan UniversityFoshan528225China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and TechnologyGuangxi UniversityNanning530005China
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Zhu W, Huang Y, Yu C. The emerging role of circRNAs on skeletal muscle development in economical animals. Anim Biotechnol 2023; 34:2778-2792. [PMID: 36052979 DOI: 10.1080/10495398.2022.2118130] [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: 11/01/2022]
Abstract
CircRNAs are a novel type of closed circular molecules formed through a covalent bond lacking a 5'cap and 3' end tail, which mainly arise from mRNA precursor. They are widely distributed in plants and animals and are characterized by stable structure, high conservativeness in cells or tissues, and showed the expression specificity at different stages of development in different tissues. CircRNAs have been gradually attracted wide attention with the development of RNA sequencing, which become a new research hotspot in the field of RNA. CircRNAs play an important role in gene expression regulation. Presently, the related circRNAs research in the regulation of animal muscle development is still at the initial stage. In this review, the formation, properties, biological functions of circRNAs were summarized. The recent research progresses of circRNAs in skeletal muscle growth and development from economic animals including livestock, poultry and fishes were introduced. Finally, we proposed a prospective for further studies of circRNAs in muscle development, and we hope our research could provide new ideas, some theoretical supports and helps for new molecular genetic markers exploitation and animal genetic breeding in future.
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Affiliation(s)
- Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Chuan Yu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
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7
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Liu S, Wu J, Zhang W, Jiang H, Zhou Y, Liu J, Mao H, Liu S, Chen B. Whole-Transcriptome RNA Sequencing Uncovers the Global Expression Changes and RNA Regulatory Networks in Duck Embryonic Myogenesis. Int J Mol Sci 2023; 24:16387. [PMID: 38003577 PMCID: PMC10671564 DOI: 10.3390/ijms242216387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Duck meat is pivotal in providing high-quality protein for human nutrition, underscoring the importance of studying duck myogenesis. The regulatory mechanisms governing duck myogenesis involve both coding and non-coding RNAs, yet their specific expression patterns and molecular mechanisms remain elusive. To address this knowledge gap, we performed expression profiling analyses of mRNAs, lncRNAs, circRNAs, and miRNAs involved in duck myogenesis using whole-transcriptome RNA-seq. Our analysis identified 1733 differentially expressed (DE)-mRNAs, 1116 DE-lncRNAs, 54 DE-circRNAs, and 174 DE-miRNAs when comparing myoblasts and myotubes. A GO analysis highlighted the enrichment of DE molecules in the extracellular region, protein binding, and exocyst. A KEGG analysis pinpointed pathways related to ferroptosis, PPAR signaling, nitrogen metabolism, cell cycle, cardiac muscle contraction, glycerolipid metabolism, and actin cytoskeleton. A total of 51 trans-acting lncRNAs, including ENSAPLT00020002101 and ENSAPLT00020012069, were predicted to participate in regulating myoblast proliferation and differentiation. Based on the ceRNAs, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks involving five miRNAs (miR-129-5p, miR-133a-5p, miR-22-3p, miR-27b-3p, and let-7b-5p) that are relevant to myogenesis. Furthermore, the GO and KEGG analyses of the DE-mRNAs within the ceRNA network underscored the significant enrichment of the glycerolipid metabolism pathway. We identified five different DE-mRNAs, specifically ENSAPLG00020001677, ENSAPLG00020002183, ENSAPLG00020005019, ENSAPLG00020010497, and ENSAPLG00020017682, as potential target genes that are crucial for myogenesis in the context of glycerolipid metabolism. These five mRNAs are integral to ceRNA networks, with miR-107_R-2 and miR-1260 emerging as key regulators. In summary, this study provides a valuable resource elucidating the intricate interplay of mRNA-lncRNA-circRNA-miRNA in duck myogenesis, shedding light on the molecular mechanisms that govern this critical biological process.
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Affiliation(s)
- Shuibing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jintao Wu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wentao Zhang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongxia Jiang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yanan Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jing Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sanfeng Liu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
| | - Biao Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China; (S.L.); (J.W.); (W.Z.); (H.J.); (Y.Z.); (J.L.); (H.M.)
- Poultry Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
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8
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Wang J, Fu Y, Su T, Wang Y, Soladoye OP, Huang Y, Zhao Z, Zhao Y, Wu W. A Role of Multi-Omics Technologies in Sheep and Goat Meats: Progress and Way Ahead. Foods 2023; 12:4069. [PMID: 38002128 PMCID: PMC10670074 DOI: 10.3390/foods12224069] [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: 09/23/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Sheep and goat meats are increasingly popular worldwide due to their superior nutritional properties and distinctive flavor profiles. In recent decades, substantial progress in meat science has facilitated in-depth examinations of ovine and caprine muscle development during the antemortem phase, as well as post-mortem changes influencing meat attributes. To elucidate the intrinsic molecular mechanisms and identify potential biomarkers associated with meat quality, the methodologies employed have evolved from traditional physicochemical parameters (such as color, tenderness, water holding capacity, flavor, and pH) to some cutting-edge omics technologies, including transcriptomics, proteomics, and metabolomics approaches. This review provides a comprehensive analysis of multi-omics techniques and their applications in unraveling sheep and goat meat quality attributes. In addition, the challenges and future perspectives associated with implementing multi-omics technologies in this area of study are discussed. Multi-omics tools can contribute to deciphering the molecular mechanism responsible for the altered the meat quality of sheep and goats across transcriptomic, proteomic, and metabolomic dimensions. The application of multi-omics technologies holds great potential in exploring and identifying biomarkers for meat quality and quality control, thereby promoting the optimization of production processes in the sheep and goat meat industry.
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Affiliation(s)
- Jin Wang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Southwest University, Chongqing 400715, China
| | - Yu Fu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Tianyu Su
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Southwest University, Chongqing 400715, China
| | - Yupeng Wang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Olugbenga P Soladoye
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Government of Canada, 6000 C&E Trail, Lacombe, AB T4L 1W1, Canada
| | - Yongfu Huang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Southwest University, Chongqing 400715, China
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Southwest University, Chongqing 400715, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Southwest University, Chongqing 400715, China
| | - Wei Wu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Southwest University, Chongqing 400715, China
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Hjazi A, Sukmana BI, Ali SS, Alsaab HO, Gupta J, Ullah MI, Romero-Parra RM, Alawadi AHR, Alazbjee AAA, Mustafa YF. Functional role of circRNAs in osteogenesis: A review. Int Immunopharmacol 2023; 121:110455. [PMID: 37290324 DOI: 10.1016/j.intimp.2023.110455] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/20/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
The extracellular matrixes (ECM), as well as the microenvironmental signals, play an essential role in osteogenesis by regulating intercellular pathways. Recently, it has been demonstrated that a newly identified RNA, circular RNA, contributes to the osteogenesis process. Circular RNA (circRNA), the most recently identified RNA, is involved in the regulation of gene expression at transcription to translation levels. The dysregulation of circRNAs has been observed in several tumors and diseases. Also, various studies have shown that circRNAs expression is changed during osteogenic differentiation of progenitor cells. Therefore, understanding the role of circRNAs in osteogenesis might help the diagnosis as well as treatment of bone diseases such as bone defects and osteoporosis. In this review, circRNA functions and the related pathways in osteogenesis have been discussed.
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Affiliation(s)
- Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Bayu Indra Sukmana
- Department of Oral Biology, Faculty of Dentistry, Lambung Mangkurat University, Banjarmasin, Indonesia
| | - Sally Saad Ali
- College of Dentistry, Al-Bayan University, Baghdad, Iraq
| | - Hashem O Alsaab
- Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, Saudi Arabia
| | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, Pin Code 281406 U.P., India
| | - Muhammad Ikram Ullah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 75471, Aljouf, Saudi Arabia
| | | | - Ahmed H R Alawadi
- Medical Analysis Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul-41001, Iraq
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10
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Ai N, Yu Z, Xu X, Liufu S, Wang K, Huang S, Li X, Liu X, Chen B, Ma H, Yin Y. Circular Intronic RNA circTTN Inhibits Host Gene Transcription and Myogenesis by Recruiting PURB Proteins to form Heterotypic Complexes. Int J Mol Sci 2023; 24:9859. [PMID: 37373006 DOI: 10.3390/ijms24129859] [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: 04/28/2023] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Muscle cell growth plays an important role in skeletal muscle development. Circular RNAs (circRNAs) have been proven to be involved in the regulation of skeletal muscle growth and development. In this study, we explored the effect of circTTN on myoblast growth and its possible molecular mechanism. Using C2C12 cells as a functional model, the authenticity of circTTN was confirmed by RNase R digestion and Sanger sequencing. Previous functional studies have showed that the overexpression of circTTN inhibits myoblast proliferation and differentiation. Mechanistically, circTTN recruits the PURB protein on the Titin (TTN) promoter to inhibit the expression of the TTN gene. Moreover, PURB inhibits myoblast proliferation and differentiation, which is consistent with circTTN function. In summary, our results indicate that circTTN inhibits the transcription and myogenesis of the host gene TTN by recruiting PURB proteins to form heterotypic complexes. This work may act as a reference for further research on the role of circRNA in skeletal muscle growth and development.
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Affiliation(s)
- Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Sui Liufu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Kaiming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shengqiang Huang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bohe Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
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11
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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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12
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Wu K, Tan J, Yang C. Recent advances and application value of circRNA in neuroblastoma. Front Oncol 2023; 13:1180300. [PMID: 37091173 PMCID: PMC10116045 DOI: 10.3389/fonc.2023.1180300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 04/09/2023] Open
Abstract
Neuroblastoma (NB) is children’s most prevalent solid malignant tumor, accounting for 15% of childhood cancer mortality. Non-coding RNA is important in NB pathogenesis. As a newly identified non-coding RNA, abnormal regulation (abnormal up-regulation or down-regulation) of the circRNAs expression is implicated in the tumorigenesis of various tumors, including NB. CircRNAs primarily regulate the expression of microRNA (miRNA) target genes by microRNA (miRNA) sponge adsorption. Clinical evidence suggests that the expression of certain circRNAs is associated with the prognosis and clinical features of NB and hence may be exploited as a biomarker or therapeutic target. This review examines circRNAs that have been demonstrated to play a function in NB.
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Affiliation(s)
- Ke Wu
- Department of Pharmacology, Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Juan Tan
- Child Healthcare Department, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Chao Yang
- Child Healthcare Department, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatric Surgical Oncology, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Chao Yang,
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13
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Lei S, Li C, She Y, Zhou S, Shi H, Chen R. Roles of super enhancers and enhancer RNAs in skeletal muscle development and disease. Cell Cycle 2023; 22:495-505. [PMID: 36184878 PMCID: PMC9928468 DOI: 10.1080/15384101.2022.2129240] [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: 07/28/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022] Open
Abstract
Skeletal muscle development is a multistep biological process regulated by a variety of myogenic regulatory factors, including MyoG, MyoD, Myf5, and Myf6 (also known as MRF4), as well as members of the FoxO subfamily. Differentiation and regeneration during skeletal muscle myogenesis contribute to the physiological function of muscles. Super enhancers (SEs) and enhancer RNAs (eRNAs) are involved in the regulation of development and diseases. Few studies have identified the roles of SEs and eRNAs in muscle development and pathophysiology. To develop approaches to enhance skeletal muscle mass and function, a more comprehensive understanding of the key processes underlying muscular diseases is needed. In this review, we summarize the roles of SEs and eRNAs in muscle development and disease through affecting of DNA methylation, FoxO subfamily, RAS-MEK signaling, chromatin modifications and accessibility, MyoD and cis regulating target genes. The summary could inform strategies to increase muscle mass and treat muscle-related diseases.
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Affiliation(s)
- Si Lei
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Cheng Li
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Yanling She
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Shanyao Zhou
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Huacai Shi
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
| | - Rui Chen
- Guangdong Second Provincial General Hospital, Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangzhou, China
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14
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Sun X, Kang Y, Li M, Li Y, Song J. The emerging regulatory mechanisms and biological function of circular RNAs in skeletal muscle development. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194888. [DOI: 10.1016/j.bbagrm.2022.194888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/07/2022]
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15
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Karami Fath M, Pourbagher Benam S, Salmani K, Naderi S, Fahham Z, Ghiabi S, Houshmand Kia SA, Naderi M, Darvish M, Barati G. Circular RNAs in neuroblastoma: Pathogenesis, potential biomarker, and therapeutic target. Pathol Res Pract 2022; 238:154094. [PMID: 36087416 DOI: 10.1016/j.prp.2022.154094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 10/15/2022]
Abstract
Neuroblastoma (NB) is a common cancer in childhood responsible for 15 % of fatalities by pediatric cancers. Epigenetic factors play an important role in the pathogenesis of NB. Recently, it has been demonstrated that circular RNAs (circRNAs, ciRNAs), a newly identified class of non-coding RNAs, are also dysregulated in NB. CircRNAs mediate their functions by regulating gene expression mainly through microRNA (miRNA) sponging. The dysregulation (abnormal upregulation or downregulation) of circRNAs is involved in tumorigenesis of a variety of tumors including NB. It seems that the expression of some circRNAs is correlated with NB prognosis and clinical features. CircRNAs might be favorable as a diagnostic/prognostic biomarker and therapeutic target. However, due to the lack of studies, it is difficult to make a conclusion regarding the clinical benefits of circRNAs. In this review, we discussed the circRNAs that experimentally have been proved to be dysregulated in NB tissues and cancer cells.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Kiana Salmani
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sina Naderi
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Fahham
- Faculty of Biology, Technische Universitat Dresden, Dresden, Germany
| | - Shamim Ghiabi
- Department of Medical Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Malihe Naderi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Maryam Darvish
- Department of Medical Biotechnology, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
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16
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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17
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Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens. Genes (Basel) 2022; 13:genes13061033. [PMID: 35741795 PMCID: PMC9222894 DOI: 10.3390/genes13061033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Chicken is the most widely consumed meat product worldwide and is a high-quality source of protein for humans. The skeletal muscle, which accounts for the majority of chicken products and contains the most valuable components, is tightly correlated to meat product yield and quality. In domestic chickens, skeletal muscle growth is regulated by a complex network of molecules that includes some non-coding RNAs (ncRNAs). As a regulator of muscle growth and development, ncRNAs play a significant function in the development of skeletal muscle in domestic chickens. Recent advances in sequencing technology have contributed to the identification and characterization of more ncRNAs (mainly microRNAs (miRNAs), long non-coding RNAs (LncRNAs), and circular RNAs (CircRNAs)) involved in the development of domestic chicken skeletal muscle, where they are widely involved in proliferation, differentiation, fusion, and apoptosis of myoblasts and satellite cells, and the specification of muscle fiber type. In this review, we summarize the ncRNAs involved in the skeletal muscle growth and development of domestic chickens and discuss the potential limitations and challenges. It will provide a theoretical foundation for future comprehensive studies on ncRNA participation in the regulation of skeletal muscle growth and development in domestic chickens.
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18
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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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LncR-133a Suppresses Myoblast Differentiation by Sponging miR-133a-3p to Activate the FGFR1/ERK1/2 Signaling Pathway in Goats. Genes (Basel) 2022; 13:genes13050818. [PMID: 35627202 PMCID: PMC9141198 DOI: 10.3390/genes13050818] [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: 04/16/2022] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 12/03/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in a variety of biological processes and illnesses. While a considerable number of lncRNAs have been discovered in skeletal muscle to far, their role and underlying processes during myogenesis remain mostly unclear. In this study, we described a new functional lncRNA named lncR-133a. Gene overexpression and interference studies in goat skeletal muscle satellite cells (MuSCs) were used to establish its function. The molecular mechanism by which lncR-133a governs muscle differentiation was elucidated primarily using quantitative real-time PCR (qRT-PCR), Western blotting, dual-luciferase activity assays, RNA immunoprecipitation, biotin-labeled probe, and RNA fluorescence in situ hybridization analyses. LncR-133a was found to be substantially expressed in longissimus thoracis et lumborum muscle, and its expression levels changed during MuSC differentiation in goats. We validated that lncR-133a suppresses MuSC differentiation in vitro. Dual-luciferase reporter screening, Argonaute 2 (AGO2) RNA immunoprecipitation assays, biotin-labeled lncR-133a capture, and fluorescence in situ hybridization showed that lncR-133a interacted with miR-133a-3p. Additionally, miR-133a-3p facilitated MuSC differentiation, but lncR-133a reversed this effect. The luciferase reporter assay and functional analyses established that miR-133a-3p directly targets fibroblast growth factor receptor 1 (FGFR1). Moreover, lncR-133a directly reduced miR-133a-3p’s capacity to suppress FGFR1 expression, and positively regulated the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). In summary, our results suggested that lncR-133a suppresses goat muscle differentiation by targeting miR-133a-3p and activating FGFR1/ERK1/2 signaling pathway.
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20
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Zhang RM, Pan Y, Zou CX, An Q, Cheng JR, Li PJ, Zheng ZH, Pan Y, Feng WY, Yang SF, Shi DS, Wei YM, Deng YF. CircUBE2Q2 promotes differentiation of cattle muscle stem cells and is a potential regulatory molecule of skeletal muscle development. BMC Genomics 2022; 23:267. [PMID: 35387588 PMCID: PMC8985345 DOI: 10.1186/s12864-022-08518-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Background The growth and development of muscle stem cells (MuSCs) are significant events known to affect muscle plasticity, disease, meat production, and meat quality, which involves the types and functions of mRNA and non-coding RNA. Here, MuSCs were cultured from Guangxi fetal cattle. RNA sequencing was used to analyze the RNA expression of mRNA and non-coding RNAs during the cell proliferation and differentiation phases. Results Two thousand one hundred forty-eight mRNAs and 888 non-coding RNAs were differentially expressed between cell proliferation and differentiation phases, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. RT-qPCR verified the differential expression levels of mRNAs and non-coding RNAs, and the differentially expressed circUBE2Q2 was subsequently characterized. Expression profile analysis revealed that circUBE2Q2 was abundant in muscle tissues and intramuscular fat. The expression of cricUBE2Q2 was also significantly upregulated during MuSCs myogenic differentiation and SVFs adipogenic differentiation and decreased with age in cattle muscle tissue. Finally, the molecular mechanism of circUBE2Q2 regulating MuSCs function that affects skeletal muscle development was investigated. The results showed that circUBE2Q2 could serve as a sponge for miR-133a, significantly promoting differentiation and apoptosis of cultured MuSCs, and inhibiting proliferation of MuSCs. Conclusions CircUBE2Q2 is associated with muscle growth and development and induces MuSCs myogenic differentiation through sponging miR-133a. This study will provide new clues for the mechanisms by which mRNAs and non-coding RNAs regulate skeletal muscle growth and development, affecting muscle quality and diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08518-4.
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Affiliation(s)
- Rui-Men Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yu Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Chao-Xia Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qiang An
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Juan-Ru Cheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Peng-Ju Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Zi-Hua Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yan Pan
- Guangxi Agricultural Vocational University, Nanning, 530007, Guangxi, China
| | - Wan-You Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Su-Fang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.,International Zhuang Medical Hospital Affiliated to Guangxi University Chinese Medicine, Nanning, 530000, Guangxi, China
| | - De-Shun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China
| | - Ying-Ming Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Yan-Fei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Animal Reproduction Institute, Guangxi University, Nanning, 530004, Guangxi, China.
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Cai B, Ma M, Zhou Z, Kong S, Zhang J, Zhang X, Nie Q. circPTPN4 regulates myogenesis via the miR-499-3p/NAMPT axis. J Anim Sci Biotechnol 2022; 13:2. [PMID: 35152912 PMCID: PMC8842800 DOI: 10.1186/s40104-021-00664-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Background Circular RNAs (circRNAs) are a novel class of endogenous ncRNA, which widely exist in the transcriptomes of different species and tissues. Recent studies indicate important roles for circRNAs in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the specific role of circRNAs in myogenesis is still poorly understood. In this study, we attempted to systematically identify the circRNAs involved in myogenesis and analyze the biological functions of circRNAs in chicken skeletal muscle development. Results In total, 532 circRNAs were identified as being differentially expressed between pectoralis major (PEM) and soleus (SOL) in 7-week-old Xinghua chicken. Among them, a novel circRNA (novel_circ_002621), generated by PTPN4 gene, was named circPTPN4 and identified. circPTPN4 is highly expressed in skeletal muscle, and its expression level is upregulated during myoblast differentiation. circPTPN4 facilitates the proliferation and differentiation of myoblast. Moreover, circPTPN4 suppresses mitochondria biogenesis and activates fast-twitch muscle phenotype. Mechanistically, circPTPN4 can function as a ceRNA to regulate NAMPT expression by sponging miR-499-3p, thus participating in AMPK signaling. Conclusions circPTPN4 functions as a ceRNA to regulate NAMPT expression by sponging miR-499-3p, thus promoting the proliferation and differentiation of myoblast, as well as activating fast-twitch muscle phenotype. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00664-1.
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22
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Ren Z, Yang Q, Guo J, Huang H, Li B, Yang Z, Tian X. Circular RNA hsa_circ_0000073 Enhances Osteosarcoma Cells Malignant Behavior by Sponging miR-1252-5p and Modulating CCNE2 and MDM2. Front Cell Dev Biol 2021; 9:714601. [PMID: 34568326 PMCID: PMC8459753 DOI: 10.3389/fcell.2021.714601] [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: 05/25/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022] Open
Abstract
Objective: An increasing number of studies have demonstrated that circular RNAs (circRNAs) are involved in tumor progression. However, the role of hsa_circ_0000073 in osteosarcoma (OS) is still not fully elucidated. Methods: Quantitative reverse transcription-polymerase chain reaction or Western blot was used to detect the gene expression. GeneChip analysis, bioinformatics, luciferase reporter, and RNA immunoprecipitation assays were adopted to predict and verify the relationships between genes. Counting Kit-8 Assay, clone formation assay, wound-healing assay, transwell assays, cell cycle assays, and in vivo tumorigenesis were used to evaluate cell function. Results: hsa_circ_0000073 was highly expressed in OS cell lines and could promote OS progression, including proliferation, migration, invasion, and cell cycle in vitro as well as tumorigenesis in vivo. Mechanically, hsa_circ_0000073 could readily downregulate the expression of CCNE2 and MDM2 through miR-1252-5p. Rescue experiments validated miR-1252-5p mimics, or CCNE2/MDM2 short hairpin RNA could reverse the hsa_circ_0000073 overexpressing-induced impairment of malignant tumor behavior. Conclusion: hsa_circ_0000073 functions as a tumor promoter in OS to increase malignant tumor behavior through sponging miR-1252-5p and regulating CCNE2 and MDM2 expression, which could be a novel target for OS therapy.
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Affiliation(s)
- Zhijing Ren
- Medical College of Guizhou University, Guiyang, China.,Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, China
| | - Qinqin Yang
- Medical College of Guizhou University, Guiyang, China
| | - Jiajia Guo
- Medical College of Guizhou University, Guiyang, China
| | - Haifeng Huang
- Department of Orthopedics, Guizhou Provincial People's Hospital, Guiyang, China
| | - Bo Li
- Department of Orthopedics, Guizhou Provincial People's Hospital, Guiyang, China
| | - Zhen Yang
- Medical College of Guizhou University, Guiyang, China.,Department of Orthopedics, Guizhou Provincial People's Hospital, Guiyang, China
| | - Xiaobin Tian
- Medical College of Guizhou University, Guiyang, China.,Department of Orthopedics, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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23
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Huang H, Xing D, Zhang Q, Li H, Lin J, He Z, Lin J. LncRNAs as a new regulator of chronic musculoskeletal disorder. Cell Prolif 2021; 54:e13113. [PMID: 34498342 PMCID: PMC8488571 DOI: 10.1111/cpr.13113] [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: 03/14/2021] [Revised: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 01/15/2023] Open
Abstract
Objectives In recent years, long non‐coding RNAs (lncRNAs) have been found to play a role in the occurrence, progression and prognosis of chronic musculoskeletal disorders. Design and methods Literature exploring on PubMed was conducted using the combination of keywords 'LncRNA' and each of the following: 'osteoarthritis', 'rheumatoid arthritis', 'osteoporosis', 'osteogenesis', 'osteoclastogenesis', 'gout arthritis', 'Kashin‐Beck disease', 'ankylosing spondylitis', 'cervical spondylotic myelopathy', 'intervertebral disc degeneration', 'human muscle disease' and 'muscle hypertrophy and atrophy'. For each disorder, we focused on the publications in the last five years (5/1/2016‐2021/5/1, except for Kashin‐Beck disease). Finally, we excluded publications that had been reported in reviews of various musculoskeletal disorders during the last three years. Here, we summarized the progress of research on the role of lncRNA in multiple pathological processes during musculoskeletal disorders. Results LncRNAs play a crucial role in regulating downstream gene expression and maintaining function and homeostasis of cells, especially in chondrocytes, synovial cells, osteoblasts, osteoclasts and skeletal muscle cells. Conclusions Understanding the mechanisms of lncRNAs in musculoskeletal disorders may provide promising strategies for clinical practice.
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Affiliation(s)
- Hesuyuan Huang
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
| | - Dan Xing
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
| | - Qingxi Zhang
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
| | - Hui Li
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
| | - Jianjing Lin
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
| | - Zihao He
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
| | - Jianhao Lin
- Arthritis Clinic & Research Center, Peking University People's Hospital, Peking University, Beijing, China.,Arthritis Institute, Peking University, Beijing, China
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24
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Zhang R, Wang J, Xiao Z, Zou C, An Q, Li H, Zhou X, Wu Z, Shi D, Deng Y, Yang S, Wei Y. The Expression Profiles of mRNAs and lncRNAs in Buffalo Muscle Stem Cells Driving Myogenic Differentiation. Front Genet 2021; 12:643497. [PMID: 34306003 PMCID: PMC8294193 DOI: 10.3389/fgene.2021.643497] [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: 12/18/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Buffalo breeding has become an important branch of the beef cattle industry. Hence, it is of great significance to study buffalo meat production and meat quality. However, the expression profiles of mRNA and long non-coding RNAs (lncRNA) molecules in muscle stem cells (MuSCs) development in buffalo have not been explored fully. We, therefore, performed mRNA and lncRNA expression profiling analysis during the proliferation and differentiation phases of MuSCs in buffalo. The results showed that there were 4,820 differentially expressed genes as well as 12,227 mRNAs and 1,352 lncRNAs. These genes were shown to be enriched in essential biological processes such as cell cycle, p53 signaling pathway, RNA transport and calcium signaling pathway. We also identified a number of functionally important genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the characteristics of mRNA and lncRNA expression during the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.
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Affiliation(s)
- Ruimen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Jinling Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Zhengzhong Xiao
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Chaoxia Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Qiang An
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Xiaoqing Zhou
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Zhuyue Wu
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Sufang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China.,International Zhuang Medical Hospital Affiliated to Guangxi University Chinese Medicine, Nanning, China
| | - Yingming Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
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25
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Bella F, Campo S. Long non-coding RNAs and their involvement in bipolar disorders. Gene 2021; 796-797:145803. [PMID: 34175394 DOI: 10.1016/j.gene.2021.145803] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/22/2021] [Indexed: 01/22/2023]
Abstract
Non-coding RNAs (nc-RNAs) can be defined as RNA molecules that are not translated into proteins. Although the functional meaning of many nc-RNAs remains still to be verified, several of these molecules have a clear biological importance, which goes from translation of mRNAs to DNA replication. Indeed, regulatory nc-RNAs can be classified into two groups: short non-coding RNAs (sncRNAs) and long-non coding RNAs (lncRNAs). In the last years, lncRNAs have gained increasing importance in the study of gene regulation, helping authors understand the molecular mechanisms underlying cellular physiology and pathology. LncRNAs are greater than 200 bp and accumulate in nucleus, cytoplasm and exosomes with high tissue specificity, acting in cis or in trans in order to exert enhancer or silencer modulation on gene expression. Such regulatory features, which are widespread in human cells and tissues, can be disrupted in several morbid states. Recent evidences may suggest a disruption of lncRNAs in bipolar disorders, a cluster of severe, chronic and disabling psychiatric diseases, which are characterized by major depressive states cyclically alternating with manic episodes. Here, the authors reviewed genes, classification, biogenesis, structures, functions and databases regarding lncRNAs, and also focused on bipolar disorders, in which some lncRNAs, especially those involved in inflammation and neuronal development, has reported to be dysregulated.
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Affiliation(s)
- Fabrizio Bella
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy
| | - Salvatore Campo
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy.
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26
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Zhao Y, Guo M. EFFECTS OF PUERARIA LOBATA COMBINED WITH HIGH-INTENSITY INTERMITTENT TRAINING ON SKELETAL MUSCLE QUALITY AND GENE EXPRESSION. REV BRAS MED ESPORTE 2021. [DOI: 10.1590/1517-8692202127022021_0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
ABSTRACT Extraction of effective components from Pueraria lobata has important value for skeletal muscle quality and gene expression. The improvement effect of traditional high-intensity intermittent training on skeletal muscle has not been obvious, and it is difficult to guarantee the properties of some volatiles. Based on this, this paper analyzes the effect of high-intensity intermittent training on skeletal muscle quality and gene expression in Pueraria lobata. Based on a brief summary of extraction of Pueraria lobata, status of research on the pharmaceutical components of Pueraria lobata was summarized. Different specimens of Pueraria lobata were selected as research objects, and the process of high-intensity intermittent training was designed. High-intensity intermittent training, solvent extraction and water solvent extraction were combined together to design the fixed-bed continuous extraction scheme. According to the influence of Pueraria lobata on skeletal muscle quality, the influence of intermittent training on skeletal muscle quality was analyzed. The extraction results showed that Pueraria lobata combined with high-intensity intermittent training can effectively improve the content of skeletal muscle and ensure the effective expression of skeletal muscle gene.
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Affiliation(s)
- Yun Zhao
- East China University of Science and Technology, China
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27
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Yan J, Yang Y, Fan X, Tang Y, Tang Z. Sp1-Mediated circRNA circHipk2 Regulates Myogenesis by Targeting Ribosomal Protein Rpl7. Genes (Basel) 2021; 12:genes12050696. [PMID: 34066653 PMCID: PMC8151578 DOI: 10.3390/genes12050696] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) represent a class of covalently closed single-stranded RNA molecules that are emerging as essential regulators of various biological processes. The circRNA circHipk2 originates from exon 2 of the Hipk2 gene in mice and was reported to be involved in acute promyelocytic leukemia and myocardial injury. However, the functions and mechanisms of circHipk2 in myogenesis are largely unknown. Here, to deepen our knowledge about the role of circHipk2, we studied the expression and function of circHipk2 during skeletal myogenesis. We found that circHipk2 was mostly distributed in the cytoplasm, and dynamically and differentially expressed in various myogenesis systems in vitro and in vivo. Functionally, overexpression of circHipk2 inhibited myoblast proliferation and promoted myotube formation in C2C12 cells, whereas the opposite effects were observed after circHipk2 knockdown. Mechanistically, circHipk2 could directly bind to ribosomal protein Rpl7, an essential 60S preribosomal assembly factor, to inhibit ribosome translation. In addition, we verified that transcription factor Sp1 directly bound to the promoter of circHipk2 and affected the expression of Hipk2 and circHipk2 in C2C12 myoblasts. Collectively, these findings identify circHipk2 as a candidate circRNA regulating ribosome biogenesis and myogenesis proliferation and differentiation.
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Affiliation(s)
- Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (J.Y.); (Y.Y.); (X.F.); (Y.T.)
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (J.Y.); (Y.Y.); (X.F.); (Y.T.)
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (J.Y.); (Y.Y.); (X.F.); (Y.T.)
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (J.Y.); (Y.Y.); (X.F.); (Y.T.)
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (J.Y.); (Y.Y.); (X.F.); (Y.T.)
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama 547500, China
- Correspondence:
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28
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Wang L, He T, Zhang X, Wang Y, Qiu K, Jiao N, He L, Yin J. Global transcriptomic analysis reveals Lnc-ADAMTS9 exerting an essential role in myogenesis through modulating the ERK signaling pathway. J Anim Sci Biotechnol 2021; 12:4. [PMID: 33526083 PMCID: PMC7852153 DOI: 10.1186/s40104-020-00524-4] [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: 06/21/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are emerging key regulators involved in a variety of biological processes such as cell differentiation and development. The balance between myogenesis and adipogenesis is crucial for skeletal muscle homeostasis in humans and meat quality in farm animals. The present study aimed to reveal the global transcriptomic profiles of adipogenic (Adi-) and myogenic (Myo-) precursors derived from porcine skeletal muscle and identify lncRNAs involved in the modulation of myogenesis homeostasis in porcine skeletal muscle. Results In this study, a total of 655 novel individual lncRNAs including differentially expressed 24 lncRNAs, and 755 differentially expressed mRNAs were identified (fold change ≥2 or ≤ 0.5 and adjusted P < 0.05). Integrated results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis accompanied by the variation of intracellular Ca2+ concentration highlighted Lnc-ADAMTS9 involved in the modulation of myogenesis homeostasis in porcine skeletal muscle. Although Lnc-ADAMTS9 knock-down did not alter the mRNA expression of ADAMTS9, we demonstrated that Lnc-ADAMTS9 can promote myogenic proliferation and myogenic differentiation of myogenic precursors through inhibiting the ERK/MAPK signaling pathway. Conclusion We deciphered a comprehensive catalog of mRNAs and lncRNAs that might be involved in the regulation of myogenesis and adipogenesis homeostasis in the skeletal muscle of pigs. The Lnc-ADAMTS9 exerts an essential role in myogenesis through the ERK signaling pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-020-00524-4.
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Affiliation(s)
- Liqi Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Ting He
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xin Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yubo Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Kai Qiu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Ning Jiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Linjuan He
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
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29
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Persson PB, Persson AB. Pregnancy. Acta Physiol (Oxf) 2021; 231:e13582. [PMID: 33220173 DOI: 10.1111/apha.13582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Pontus B. Persson
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt‐Universität zu Berlin, and Berlin Institute of Health Institute of Vegetative Physiology Berlin Germany
| | - Anja B. Persson
- Charité – Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humboldt‐Universität zu Berlin, and Berlin Institute of Health Berlin Germany
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30
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Jiang X, Chen D. Circular RNA hsa_circ_0000658 inhibits osteosarcoma cell proliferation and migration via the miR-1227/IRF2 axis. J Cell Mol Med 2020; 25:510-520. [PMID: 33264494 PMCID: PMC7810968 DOI: 10.1111/jcmm.16105] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma (OS) is the most frequently occurring bone cancer. Circular RNAs (circRNAs) have been shown to exert pivotal impact in modulation of gene expression, but their roles in OS are still not fully understood. In this study, we analysed the role of circ‐0000658 in OS. Thereafter, molecular techniques such as Western blot, qRT‐PCR, RNA‐binding protein immunoprecipitation and Dual‐Luciferase reporter assays were implemented to investigate the role of circ‐0000658/miR‐1227/interferon regulatory factor‐2 (IRF2) axis in OS. Eventually, the impact of circ‐0000658 on tumour growth and metastasis was observed in a xenograft mouse model. The results of this study revealed that circ‐0000658 exhibits low levels in OS tissues and cell lines. Moreover, circ‐0000658 repression promoted cell cycle, proliferation, invasion and migration but inhibited the apoptosis of OS cells. Researches have previously shown that circ‐0000658 contains a binding site for miR‐1227 and thus can abundantly sponge miR‐1227 to up‐regulate the expression of its target gene IRF2. Moreover, both inhibition of miR‐1227 and overexpression of IRF2 reversed cell proliferation and invasion, which was triggered by circ‐0000658 repression. Conclusively, circ‐0000658 modulates biological function of OS cells through the miR‐1227/IRF2 axis. Therefore, circ‐0000658 might act as a possible novel therapeutic target for the treatment of OS.
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Affiliation(s)
- Xin Jiang
- Department of Orthopedics, China-Japan Friendship Hospital, Beijing, China
| | - Dong Chen
- Department of Orthopedics, China-Japan Friendship Hospital, Beijing, China
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31
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Chen R, Lei S, Jiang T, She Y, Shi H. Regulation of Skeletal Muscle Atrophy in Cachexia by MicroRNAs and Long Non-coding RNAs. Front Cell Dev Biol 2020; 8:577010. [PMID: 33043011 PMCID: PMC7523183 DOI: 10.3389/fcell.2020.577010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle atrophy is a common complication of cachexia, characterized by progressive bodyweight loss and decreased muscle strength, and it significantly increases the risks of morbidity and mortality in the population with atrophy. Numerous complications associated with decreased muscle function can activate catabolism, reduce anabolism, and impair muscle regeneration, leading to muscle wasting. microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), types of non-coding RNAs, are important for regulation of skeletal muscle development. Few studies have specifically identified the roles of miRNAs and lncRNAs in cellular or animal models of muscular atrophy during cachexia, and the pathogenesis of skeletal muscle wasting in cachexia is not entirely understood. To develop potential approaches to improve skeletal muscle mass, strength, and function, a more comprehensive understanding of the known key pathophysiological processes leading to muscular atrophy is needed. In this review, we summarize the known miRNAs, lncRNAs, and corresponding signaling pathways involved in regulating skeletal muscle atrophy in cachexia and other diseases. A comprehensive understanding of the functions and mechanisms of miRNAs and lncRNAs during skeletal muscle wasting in cachexia and other diseases will, therefore, promote therapeutic treatments for muscle atrophy.
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Affiliation(s)
- Rui Chen
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Si Lei
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Ting Jiang
- Department of Radiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanling She
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Huacai Shi
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou, China
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32
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Di Agostino S, Riccioli A, De Cesaris P, Fontemaggi G, Blandino G, Filippini A, Fazi F. Circular RNAs in Embryogenesis and Cell Differentiation With a Focus on Cancer Development. Front Cell Dev Biol 2020; 8:389. [PMID: 32528957 PMCID: PMC7266935 DOI: 10.3389/fcell.2020.00389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
In the recent years thousands of non-coding RNAs have been identified, also thanks to highthroughput sequencing technologies. Among them, circular RNAs (circRNAs) are a well-represented class characterized by the high sequence conservation and cell type specific expression in eukaryotes. They are covalently closed loops formed through back-splicing. Recently, circRNAs were shown to regulate a variety of cellular processes functioning as miRNA sponges, RBP binding molecules, transcriptional regulators, scaffold for protein translation, as well as immune regulators. A growing number of studies are showing that deregulated expression of circRNAs plays important and decisive actions during the development of several human diseases, including cancer. The research on their biogenesis and on the various molecular mechanisms in which they are involved is going very fast, however, there are still few studies that address their involvement in embryogenesis and eukaryotic development. This review has the intent to describe the most recent progress in the study of the biogenesis and molecular activities of circRNAs providing insightful information in the field of embryogenesis and cell differentiation. In addition, we describe the latest research on circRNAs as novel promising biomarkers in diverse types of tumors.
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Affiliation(s)
- Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Anna Riccioli
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Paola De Cesaris
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Antonio Filippini
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy.,Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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