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Bin Li, Yan R, Liu X, Meng Z, Meng P, Wang Y, Huang Y. CircRNAs Biogenesis, Functions, and Its Research Progress in Aquaculture. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022020042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2
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Zhuang X, Lin Z, Xie F, Luo J, Chen T, Xi Q, Zhang Y, Sun J. Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages. BMC Genomics 2022; 23:294. [PMID: 35410129 PMCID: PMC9004053 DOI: 10.1186/s12864-022-08515-7] [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: 08/28/2021] [Accepted: 03/29/2022] [Indexed: 11/28/2022] Open
Abstract
Background Long-term artificial selection for growth rate and lean meat rate has eventually led to meat quality deterioration. Muscle fiber type is a key factor that markedly affects meat quality. circRNAs have been reported to participate in diverse biological activities, including myofiber growth and development; thus, we herein compared porcine circRNA transcriptome between oxidative and glycolytic muscle tissues. Results Longissimus thoracis muscle tissues were obtained from Lantang and Landrace pigs at birth (LT1D and LW1D, respectively) and 90 postnatal days (LT90D and LW90D, respectively). Hematoxylin and eosin staining and quantitative real-time PCR revealed that all structural traits of the muscle showed large variations between different breeds and growth stages. In total, 329 known miRNAs and 42,081 transcript candidates were identified; 6,962 differentially expressed transcripts were found to play a key role in myogenesis by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In addition, 3,352 circRNAs were identified using five predicting algorithms, and 104 circRNA candidates were differentially expressed. Integrated analysis of differentially expressed miRNAs, mRNAs, and circRNAs led to the identification of 777, 855, and 22 convincing ceRNA interactions in LT1D vs. LT90D, LW1D vs. LW90D, and LT90D vs. LW90D, respectively. Finally, we identified a circRNA candidate circKANSL1L, which showed high homology between mice and pigs, and it was found to inhibit the proliferation of C2C12 cells but promote their differentiation. Conclusions We identified genome-wide circRNAs in 0- and 90-day-old Lantang and Landrace pigs by RNA-seq and found that circRNAs were abundant, differentially expressed, and associated with myogenesis. Our results should serve as a reference for future studies on pork quality. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08515-7.
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Affiliation(s)
- Xiaona Zhuang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Zekun Lin
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Fang Xie
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Junyi Luo
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qianyun Xi
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yongliang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jiajie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Liang Y, Gao Q, Wang H, Guo M, Arbab AAI, Nazar M, Li M, Yang Z, Karrow NA, Mao Y. Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation. Biomolecules 2022; 12:478. [PMID: 35327670 PMCID: PMC8946036 DOI: 10.3390/biom12030478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
In this study, circular RNAs (circRNAs) from Holstein cow mammary tissues were identified and compared between early lactation and non-lactation. After analysis, 10,684 circRNAs were identified, ranging from 48 to 99,406 bp, and the average size was 882 bp. The circRNAs were mainly distributed on chromosomes 1 to 11, and 89.89% of the circRNAs belonged to sense-overlapping circRNA. The exons contained with circRNAs ranged from 1 to 47 and were concentrated from 1 to 5. Compared with the non-lactating cows, 87 circRNAs were significantly differentially expressed in the peak lactation cows. There were 68 upregulated circRNAs and 19 downregulated circRNAs. Enrichment analysis of circRNAs showed that GO analysis mainly focused on immune response, triglyceride transport, T cell receptor signaling pathway, etc. Pathway analysis mainly focused on cytokine-cytokine receptor interaction, T helper 17 cell differentiation, fatty acid biosynthesis, the JAK-STAT signaling pathway, etc. Specific primers were designed for two proximal ends of the circRNA junction sites to allow for PCR validation of four randomly selected circRNAs and carry out circRNA-miRNA interaction research. This study revealed the expression profile and characteristics of circRNAs in mammary tissue from Holstein cows at early lactation and non-lactation, thus providing rich information for the study of circRNA functions and mechanisms, as well as potential candidate miRNA genes for studying lactation in Holstein cows.
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Affiliation(s)
- Yan Liang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Qisong Gao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
| | - Haiyang Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
| | - Mengling Guo
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
| | - Abdelaziz Adam Idriss Arbab
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
- Biomedical Research Institute, Darfur University College, Nyala 63313, Sudan
| | - Mudasir Nazar
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
| | - Mingxun Li
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
| | - Zhangping Yang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Niel A. Karrow
- Center for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Yongjiang Mao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.L.); (Q.G.); (H.W.); (M.G.); (A.A.I.A.); (M.N.); (M.L.); (Z.Y.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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The Competitive Endogenous RNA (ceRNA) Regulation in Porcine Alveolar Macrophages (3D4/21) Infected by Swine Influenza Virus (H1N1 and H3N2). Int J Mol Sci 2022; 23:ijms23031875. [PMID: 35163797 PMCID: PMC8836399 DOI: 10.3390/ijms23031875] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 02/08/2023] Open
Abstract
H1N1 and H3N2 are the two most common subtypes of swine influenza virus (SIV). They not only endanger the pig industry, but are also a huge risk of zoonotic diseases. However, the molecular mechanism and regulatory network of pigs (hosts) against influenza virus infection are still unclear. In this study, porcine alveolar macrophage cell (3D4/21) models infected by swine influenza virus (H1N1 and H3N2) were constructed. The expression profiles of miRNAs, mRNAs, lncRNAs and circRNAs after H1N1 and H3N2 infected 3D4/21 cells were revealed in this study. Then, two ceRNAs (TCONS_00166432-miR10391-MAN2A1 and novel_circ_0004733-miR10391-MAN2A1) that regulated H1N1 and H3N2 infection in 3D4/21 cells were verified by the methods of bioinformatics analysis, gene overexpression, gene interference, real-time quantitative PCR (qPCR), dual luciferase activity assay and RNA immunoprecipitation (RIP). In addition, the important candidate molecules (miR-10391, TCONS_00166432, and novel_circ_0004733) were identified by qPCR and enzyme linked immunosorbent assay (ELISA). Finally, the regulatory effect and possible molecular mechanism of the target gene MAN2A1 were identified by the methods of gene interference, qPCR, Western blot and ELISA. The results of this study suggested that TCONS_00166432 and novel_circ_0004733 could competitively bind miR-10391 to target the MAN2A1 gene to regulate swine influenza virus infecting 3D4/21 cells. This study reported for the first time the ceRNA networks involved in the regulation of the swine influenza virus infecting 3D4/21 cells, which provided a new insight into the molecular mechanism of 3D4/21 cells against swine influenza virus infection.
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Zhang X, Zhang C, Yang C, Kuang L, Zheng J, Tang L, Lei M, Li C, Ren Y, Guo Z, Ji Y, Deng X, Huang D, Wang G, Xie X. Circular RNA, microRNA and Protein Profiles of the Longissimus Dorsi of Germany ZIKA and Sichuan White Rabbits. Front Genet 2022; 12:777232. [PMID: 35003217 PMCID: PMC8740122 DOI: 10.3389/fgene.2021.777232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Due to the dietetic properties and remarkable nutritive value of rabbit meat, its industry is increasing rapidly. However, the association between circular RNAs, microRNAs, and proteins and muscle fiber type, and meat quality of rabbit is still unknown. Here, using deep sequencing and iTRAQ proteomics technologies we first identified 3159 circRNAs, 356 miRNAs, and 755 proteins in the longissimus dorsi tissues from Sichuan white (SCWrabs) and Germany great line ZIKA rabbits (ZIKArabs). Next, we identified 267 circRNAs, 3 miRNAs, and 29 proteins differentially expressed in the muscle tissues of SCWrabs and ZIKArabs. Interaction network analysis revealed some key regulation relationships between noncoding RNAs and proteins that might be associated with the muscle fiber type and meat quality of rabbit. Further, miRNA isoforms and gene variants identified in SCWrabs and ZIKArabs revealed some pathways and biological processes related to the muscle development. This is the first study of noncoding RNA and protein profiles for the two rabbit breeds. It provides a valuable resource for future studies in rabbits and will improve our understanding of the molecular regulation mechanisms in the muscle development of livestock. More importantly, the output of our study will benefit the researchers and producers in the rabbit breeding program.
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Affiliation(s)
- Xiangyu Zhang
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Cuixia Zhang
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Chao Yang
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Liangde Kuang
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Jie Zheng
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Li Tang
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Min Lei
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Congyan Li
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Yongjun Ren
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhiqiang Guo
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Yang Ji
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | | | - Dengping Huang
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Xiaohong Xie
- Sichuan Animal Sciences Academy, Chengdu, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, China
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6
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Cao H, Liu J, Du T, Liu Y, Zhang X, Guo Y, Wang J, Zhou X, Li X, Yang G, Shi X. Circular RNA screening identifies circMYLK4 as a regulator of fast/slow myofibers in porcine skeletal muscles. Mol Genet Genomics 2021; 297:87-99. [PMID: 34786637 PMCID: PMC8803689 DOI: 10.1007/s00438-021-01835-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/03/2021] [Indexed: 11/25/2022]
Abstract
The type of myofiber is related to the quality of meat. The slow oxidized myofiber helps to increase the tenderness and juiciness of muscle. Numerous studies have shown that circRNA plays a key role in skeletal muscle development. However, the role of circRNA in porcine skeletal myofiber types is unclear. In this study, we performed high-throughput RNA sequencing to study the differential expression of circRNA in the longissimus dorsi and the soleus muscle. A total of 40,757 circRNAs were identified, of which 181 were significantly different. Interestingly, some circRNAs were involved in metabolism pathways, AMPK, FoxO, and PI3K-Akt signaling pathways. Besides, we focused on a novel circRNA-circMYLK4. By injecting circMYLK4-AAV into piglets, we found that circMYLK4 significantly increased the mRNA and protein levels of the slow muscle marker genes. In summary, our study laid an essential foundation for further research of circRNA in myofiber type conversion and higher meat quality.
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Affiliation(s)
- Haigang Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Jieming Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Tianning Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yihao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Xiaoyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yuan Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Jie Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Xiaomin Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Xiao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China
| | - Xin'e Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China.
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Xianyang, 712100, Shaanxi, China.
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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Integrated Analysis Reveals a lncRNA-miRNA-mRNA Network Associated with Pigeon Skeletal Muscle Development. Genes (Basel) 2021; 12:genes12111787. [PMID: 34828393 PMCID: PMC8625974 DOI: 10.3390/genes12111787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA-miRNA-mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA-miRNA-mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA-miRNA-mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs TCONS_00066712, TCONS_00026594, TCONS_00001557, TCONS_00001553, and TCONS_00003307 were identified as hub genes in the ceRNA network. lncRNA TCONS_00026594 might regulate the FSHD region gene 1 (FRG1)/ SRC proto-oncogene, non-receptor tyrosine kinase (SRC) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development.
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Spatiotemporal Regulation and Functional Analysis of Circular RNAs in Skeletal Muscle and Subcutaneous Fat during Pig Growth. BIOLOGY 2021; 10:biology10090841. [PMID: 34571718 PMCID: PMC8465536 DOI: 10.3390/biology10090841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022]
Abstract
Recently, thousands of circular RNAs have been reported in different pig breeds. However, researches on the temporal and spatial expression patterns of circRNA over the period of animal growth are limited. Here, we systematically analyzed circRNAs in skeletal muscle and subcutaneous fat in four growth time points (30 days, 90 days, 150 days and 210 days after birth) of a Chinese native pig breed, Ningxiang pigs. A total of 1171 differentially expressed (DE) circRNAs between muscle and fat were identified, including 562 upregulated and 609 downregulated circRNAs. KEGG pathway enrichment analysis of these DE circRNAs revealed that host genes were mainly involved in glycogen metabolism signaling pathways, muscle development signaling pathways such as ErbB pathway and adipocytokine signaling pathways and AMPK signaling pathways and fatty acid biosynthesis. The circRNAs have striking spatiotemporal specificity in the form of dynamic expression at 90 d. Short Time-Series Expression Miner analysis showed multiple model spectra that are significantly enriched with time changes in muscle and fat. Our findings provide new ideas and perspectives about the role of circular RNAs and their targeting relations with mRNA and miRNA in skeletal muscle and fat tissue during pig growth.
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10
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Yang XM, Liang Y, Zhong ZJ, Tao X, Yang YK, Zhang P, Wang Y, Lei YF, Chen XH, Zeng K, Gong JJ, Ying SC, Zhang JL, Pang JH, Lv XB, Gu YR, He ZP. Comparison of long non-coding RNAs in adipose and muscle tissues between seven indigenous Chinese and the Yorkshire pig breeds. Anim Genet 2021; 52:645-655. [PMID: 34324723 DOI: 10.1111/age.13123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/01/2022]
Abstract
lncRNAs play crucial roles in fat metabolism in animals. Previously, we have compared the mRNA transcriptome profiles between seven fat-type Chinese pig breeds and one lean-type Western breed (Yorkshire, YY). The associations between differentially expressed (DE) genes and phenotypical traits were investigated. In the present study, to further explore the underlying regulatory mechanisms, lncRNAs were sequenced and compared between YY and Chinese indigenous breeds. The results showed 9114 and 7538 DE lncRNAs between at least one Chinese breed and the YY breed in the adipose and muscle tissue respectively. KEGG enrichment analysis revealed that the target genes of these DE lncRNAs mainly influenced the glucolipid metabolism, which is an important process affecting meat quality. Correlation analyses between the DE lncRNA and DE mRNA genes related to meat quality and growth traits were performed. The results showed that LTCONS_00073280 was associated with intramuscular fat content. Four lncRNAs (LTCONS_00101781, LTCONS_00037879, LTCONS_00088260 and LTCONS-00128343) might mediate backfat thickness. Overall, this study provides candidate lncRNAs that potentially affect meat quality, which might be useful for molecular breeding of pig breeds in future.
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Affiliation(s)
- X-M Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Z-J Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-K Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - P Zhang
- Chengdu Agricultural Technology Vocational College, Chengdu, Sichuan, 610000, China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-F Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - X-H Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - S-C Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-L Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-H Pang
- Chengdu Biotechservice Institute, Chengdu, Sichuan, 610000, China
| | - X-B Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-R Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Z-P He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
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11
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Fang C, Guo F, Zhao X, Zhang Z, Lu J, Pan H, Xu T, Li W, Yang M, Huang Y, Zhao Y, Zhao S. Biological mechanisms of growth performance and meat quality in porcine muscle tissue. Anim Biotechnol 2021; 33:1246-1254. [PMID: 33704018 DOI: 10.1080/10495398.2021.1886939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Growth performance and meat quality are important traits for pig production. The aim of the present study was to investigate the molecular mechanisms underlying growth performance and meat quality, and to identify novel target molecules for predicting the growth performance and meat quality. The differentially expressed genes (DEGs) in Diannan small ears pigs (DSP) and Landrace pigs (LP) were assessed by RNA-sequencing analyzing technology. A total of 339 DEGs were obtained between DSP and LP. 146 DEGs were upregulated in LP compared with DSP and 193 DEGs were upregulated in DSP compared with LP. The DEGs were significantly enriched in 26 GO and 3 KEGG pathways. The protein-protein interaction (PPI) network with 201 nodes and 382 edges was constructed and 5 modules were extracted from the entire network. The identified upregulated expression of genes involved in glycolysis and myogenesis as well as extracellular matrix may be associated with fast body and muscle deposition rates in LP. Increased expression of genes involved in PPAR signaling pathway and fatty acid metabolism as well as oxidative phosphate processes could be related to the intramuscular fat deposition and meat quality in DSP. The present study may provide an improved understanding of the growth performance and meat quality.
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Affiliation(s)
- Chen Fang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Fei Guo
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Xiaoqi Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China.,Institute of Herbivorous Livestock, Yunnan Academy of Animal Sciences, Kunming, China
| | - Zining Zhang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Junlan Lu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Hongbin Pan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Taojie Xu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Minghua Yang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Ying Huang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Yanguang Zhao
- Research Institute of Pig and Animal Nutrition, Yunnan Academy of Animal Sciences, Kunming, China
| | - Sumei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
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12
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Yang Z, He T, Chen Q. The Roles of CircRNAs in Regulating Muscle Development of Livestock Animals. Front Cell Dev Biol 2021; 9:619329. [PMID: 33748107 PMCID: PMC7973088 DOI: 10.3389/fcell.2021.619329] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/18/2021] [Indexed: 12/25/2022] Open
Abstract
The muscle growth and development of livestock animals is a complex, multistage process, which is regulated by many factors, especially the genes related to muscle development. In recent years, it has been reported frequently that circular RNAs (circRNAs) are involved widely in cell proliferation, cell differentiation, and body development (including muscle development). However, the research on circRNAs in muscle growth and development of livestock animals is still in its infancy. In this paper, we briefly introduce the discovery, classification, biogenesis, biological function, and degradation of circRNAs and focus on the molecular mechanism and mode of action of circRNAs as competitive endogenous RNAs in the muscle development of livestock and poultry. In addition, we also discuss the regulatory mechanism of circRNAs on muscle development in livestock in terms of transcription, translation, and mRNAs. The purpose of this article is to discuss the multiple regulatory roles of circRNAs in the process of muscle development in livestock, to provide new ideas for the development of a new co-expression regulation network, and to lay a foundation for enriching livestock breeding and improving livestock economic traits.
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Affiliation(s)
- Zhenguo Yang
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Tianle He
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qingyun Chen
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
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13
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Functional Role of circRNAs in the Regulation of Fetal Development, Muscle Development, and Lactation in Livestock. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5383210. [PMID: 33688493 PMCID: PMC7914090 DOI: 10.1155/2021/5383210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 01/23/2021] [Accepted: 02/05/2021] [Indexed: 01/04/2023]
Abstract
circRNAs are a class of endogenous noncoding RNA molecules with closed loop structures. They are mainly responsible for regulating gene expression in eukaryotic cells. With the emergence of high-throughput RNA sequencing (RNA-Seq) and new types of bioinformatics tools, thousands of circRNAs have been discovered, making circRNA one of the research hotspots. Recent studies have shown that circRNAs play an important regulatory role in the growth, reproduction, and formation of livestock products. They can not only regulate mammalian fetal growth and development but also have important regulatory effects on livestock muscle development and lactation. In this review, we briefly introduce the putative biogenic pathways and regulatory functions of circRNA and highlight our understanding of circRNA and its latest advances in fetal development, muscle development, and lactation biogenesis as well as expression in livestock. This review will provide a theoretical basis for the research and development of related industries.
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14
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Tang Y, Bao J, Hu J, Liu L, Xu DY. Circular RNA in cardiovascular disease: Expression, mechanisms and clinical prospects. J Cell Mol Med 2020; 25:1817-1824. [PMID: 33350091 PMCID: PMC7882961 DOI: 10.1111/jcmm.16203] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/15/2020] [Accepted: 12/03/2020] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are a group of covalently closed, endogenous, non‐coding RNAs, which exist widely in human tissues including the heart. Increasing evidence has shown that cardiac circRNAs play crucial regulatory roles in cardiovascular diseases (CVDs). In this review, we aimed to provide a systemic understanding of circRNAs with a special emphasis on the cardiovascular system. We have summarized the current research on the classification, biogenesis and properties of circRNAs as well as their participation in the pathogenesis of CVDs. CircRNAs are conserved, stable and have specific spatiotemporal expression; thus, they have been accepted as a potential diagnostic marker or an incremental prognostic biomarker for CVDs.
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Affiliation(s)
- Ying Tang
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jinghui Bao
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiahui Hu
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Leiling Liu
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Dan-Yan Xu
- Department of Internal Cardiovascular Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
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15
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Li B, Feng C, Zhu S, Zhang J, Irwin DM, Zhang X, Wang Z, Zhang S. Identification of Candidate Circular RNAs Underlying Intramuscular Fat Content in the Donkey. Front Genet 2020; 11:587559. [PMID: 33424924 PMCID: PMC7793956 DOI: 10.3389/fgene.2020.587559] [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: 07/26/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022] Open
Abstract
Intramuscular fat (IMF) content is a crucial indicator of meat quality. Circular RNAs (circRNAs) are a large class of endogenous RNAs that are involved in many physiological processes. However, the expression and function of circRNA in IMF in the donkey remains unresolved. Here we performed an expression profiling of circRNAs in the donkey longissimus dorsi muscle and identified 12,727 candidate circRNAs. Among these, 70% were derived from the exons of protein genes. Furthermore, a total of 127 differentially expressed (DE) circRNAs were identified in high (H) and low (L) IMF content groups, including 63 upregulated and 64 downregulated circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the host genes of the DE circRNAs showed that the host genes were enriched in lipid metabolism related GO terms (e.g., fatty acid beta-oxidation using acyl-CoA dehydrogenase and MLL3/4 complex), and signaling pathways (e.g., TGF-beta and lysine degradation signaling pathway). Further analyses indicated that 127 DE circRNAs were predicted to potentially interact with miRNAs, leading to the construction of circRNA-miRNA regulatory network. Multiple circRNAs can potentially function as sponges of miRNAs that regulate the differentiation of adipocytes. Our results provide valuable expression profile information for circRNA in the donkey and new insight into the regulatory mechanisms of circRNAs in the regulation of IMF content.
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Affiliation(s)
- Bojiang Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Feng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shiyu Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xiaoying Zhang
- Liaoning Province Engineering Center of Modern Agricultural Production Base, Shenyang, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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16
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Peng K, Jiang P, Du Y, Zeng D, Zhao J, Li M, Xia C, Xie Z, Wu J. Oxidized low-density lipoprotein accelerates the injury of endothelial cells via circ-USP36/miR-98-5p/VCAM1 axis. IUBMB Life 2020; 73:177-187. [PMID: 33249762 DOI: 10.1002/iub.2419] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022]
Abstract
Circular RNAs (circRNAs) are a group of RNAs featured by a covalently closed continuous loop structure. This study aimed to uncover the function and mechanism of circ-ubiquitin specific peptidase 36 (USP36) in endothelial cells treated with oxidized low-density lipoprotein (ox-LDL). The levels of circ-USP36, microRNA-98-5p (miR-98-5p) and vascular cell adhesion molecule 1 (VCAM1) were examined by a quantitative real-time polymerase chain reaction (qRT-PCR). The viability, apoptosis and inflammation were detected by (4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, flow cytometry and enzyme-linked immunosorbent assay (ELISA), respectively. Western blot assay was performed to detect the expression of apoptosis and proliferation-related markers and VCAM1 protein level. The targets of circ-USP36 and miR-98-5p were searched using starBase website, and dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were applied to validate the above predictions. Ox-LDL exposure induced the upregulation of circ-USP36 in HUVEC cells. Circ-USP36 accelerated ox-LDL-induced apoptosis, inflammatory and viability inhibition of HUVEC cells. MiR-98-5p was a direct downstream gene of circ-USP36. Circ-USP36 promoted the injury of ox-LDL-induced HUVEC cells through targeting miR-98-5p. VCAM1 could bind to miR-98-5p, and the protective effects of miR-98-5p accumulation on ox-LDL-induced HUVEC cells were reversed by the transfection of VCAM1. VCAM1 was regulated by circ-USP36/miR-98-5p signaling in HUVEC cells. Ox-LDL promoted the apoptosis and inflammation but suppressed the viability of HUVEC cells through upregulating circ-USP36, thus elevating the expression of VCAM1 via miR-98-5p.
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Affiliation(s)
- Kuang Peng
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Peiyong Jiang
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Yafang Du
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Dianmei Zeng
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Junbi Zhao
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Meiling Li
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Chunchen Xia
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Zhong Xie
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Jie Wu
- Department of Cardiology, The First Affiliated Hospital of University of South China, Hengyang, China
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Wang J, Chen MY, Chen JF, Ren QL, Zhang JQ, Cao H, Xing BS, Pan CY. LncRNA IMFlnc1 promotes porcine intramuscular adipocyte adipogenesis by sponging miR-199a-5p to up-regulate CAV-1. BMC Mol Cell Biol 2020; 21:77. [PMID: 33148167 PMCID: PMC7640402 DOI: 10.1186/s12860-020-00324-8] [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: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 02/08/2023] Open
Abstract
Background Local Chinese local pig breeds have thinner muscle fiber and higher intramuscular-fat (IMF) content. But its regulation mechanism has not been discussed in-depth. Studies indicated that long non coding RNAs (lncRNAs) play important role in muscle and fat development. Results The lncRNAs expressional differences in the longissimus dorsi (LD) muscle were identified between Huainan pigs (local Chinese pigs, fat-type, HN) and Large White pigs (lean-type, LW) at 38, 58, and 78 days post conception (dpc). In total, 2131 novel lncRNAs were identified in 18 samples, and 291, 305, and 683 differentially expressed lncRNAs (DELs) were found between these two breeds at three stages, respectively. The mRNAs that co-expressed with these DELs were used for GO and KEGG analysis, and the results showed that muscle development and energy metabolism were more active at 58 dpc in HN, but at 78 dpc in LW pigs. Muscle cell differentiation and myofibril assembly might associated with earlier myogenesis and primary-muscle-fiber assembly in HN, and cell proliferation, insulin, and the MAPK pathway might be contribute to longer proliferation and elevated energy metabolism in LW pigs at 78 dpc. The PI3K/Akt and cAMP pathways were associated with higher IMF deposition in HN. Intramuscular fat deposition-associated long noncoding RNA 1 (IMFlnc1) was selected for functional verification, and results indicated that it regulated the expressional level of caveolin-1 (CAV-1) by acting as competing endogenous RNA (ceRNA) to sponge miR-199a-5p. Conclusions Our data contributed to understanding the role of lncRNAs in porcine-muscle development and IMF deposition, and provided valuable information for improving pig-meat quality. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-020-00324-8.
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Affiliation(s)
- Jing Wang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Ming-Yue Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, College of Animal Science and Technology, Northwest A&F University, Ministry of Agriculture, Number 22, Xi Nong Road, Yangling, 712100, Shaanxi, China
| | - Jun-Feng Chen
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Qiao-Ling Ren
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Jia-Qing Zhang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Hai Cao
- Henan Xing Rui Agriculture and Animal Husbandry Technology Co., LTD, Number 59, Jie Fang Road, Xinxian, Xinyang, 465550, China
| | - Bao-Song Xing
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China.
| | - Chuan-Ying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, College of Animal Science and Technology, Northwest A&F University, Ministry of Agriculture, Number 22, Xi Nong Road, Yangling, 712100, Shaanxi, China.
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18
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Huang Y, Wang Y, Zhang C, Sun X. Biological functions of circRNAs and their progress in livestock and poultry. Reprod Domest Anim 2020; 55:1667-1677. [DOI: 10.1111/rda.13816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Yong Huang
- College of Animal Science and Technology Henan University of Science and Technology Luoyang China
| | - Yanli Wang
- Development Planning Office Henan University of Science and Technology Luoyang China
| | - Cai Zhang
- College of Animal Science and Technology Henan University of Science and Technology Luoyang China
| | - Xihong Sun
- Development Planning Office Henan University of Science and Technology Luoyang China
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19
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Zhang H, Hu B, Xiong J, Chen T, Xi Q, Luo J, Jiang Q, Sun J, Zhang Y. Genomewide analysis of circular RNA in pituitaries of normal and heat-stressed sows. BMC Genomics 2019; 20:1013. [PMID: 31870281 PMCID: PMC6929353 DOI: 10.1186/s12864-019-6377-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 12/08/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate animals' response to heat stress which can be easily induced by hyperthermia in summer. However, the expression and functions of circRNAs in the pituitary of sows and whether they participate in heat stress adaption are still unclear. RESULTS In this study, we found that high temperature over the thermoneutral zone of sows during the summer increased the serum heat shock protein 70 (HSP70) level, decreased the superoxide dismutase (SOD) vitality and prolactin (PRL) concentration, and induced heat stress in sows. Then, we explored circRNA in the pituitary of heat-stressed and normal sows using RNA sequencing and bioinformatics analysis. In total, 12,035 circRNAs were detected, with 59 circRNAs differentially expressed, including 42 up-regulated and 17 down-regulated circRNAs in pituitaries of the heat-stressed sows. Six randomly selected circRNAs were identified through reverse transcription PCR followed by DNA sequencing and other 7 randomly selected differentially expressed circRNAs were verified by quantitative real-time PCR analysis. The predicted target genes regulated by circRNAs through sponging microRNAs (miRNAs) were enriched in metabolic pathway. Furthermore, the predicted circRNA-miRNA-mRNA interactions showed that some circRNAs might sponge miRNAs to regulate pituitary-specific genes and heat shock protein family members, indicating circRNA's roles in pituitary hormone secretion and heat stress response. CONCLUSIONS Our results provided a meaningful reference to understand the functions of circRNA in the porcine pituitary and the mechanisms by which circRNA may participate in animals' response to heat stress.
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Affiliation(s)
- Haojie Zhang
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Baoyu Hu
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Jiali Xiong
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Ting Chen
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Qianyun Xi
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Junyi Luo
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Qingyan Jiang
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Jiajie Sun
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China.
| | - Yongliang Zhang
- Guangdong Province Key Laboratory of Animal Nutritional Regulation, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, Guangdong, 510642, People's Republic of China.
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20
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Functions and Regulatory Mechanisms of lncRNAs in Skeletal Myogenesis, Muscle Disease and Meat Production. Cells 2019; 8:cells8091107. [PMID: 31546877 PMCID: PMC6769631 DOI: 10.3390/cells8091107] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/04/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Myogenesis is a complex biological process, and understanding the regulatory network of skeletal myogenesis will contribute to the treatment of human muscle related diseases and improvement of agricultural animal meat production. Long noncoding RNAs (lncRNAs) serve as regulators in gene expression networks, and participate in various biological processes. Recent studies have identified functional lncRNAs involved in skeletal muscle development and disease. These lncRNAs regulate the proliferation, differentiation, and fusion of myoblasts through multiple mechanisms, such as chromatin modification, transcription regulation, and microRNA sponge activity. In this review, we presented the latest advances regarding the functions and regulatory activities of lncRNAs involved in muscle development, muscle disease, and meat production. Moreover, challenges and future perspectives related to the identification of functional lncRNAs were also discussed.
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21
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Liang Y, Wang Y, Ma L, Zhong Z, Yang X, Tao X, Chen X, He Z, Yang Y, Zeng K, Kang R, Gong J, Ying S, Lei Y, Pang J, Lv X, Gu Y. Comparison of microRNAs in adipose and muscle tissue from seven indigenous Chinese breeds and Yorkshire pigs. Anim Genet 2019; 50:439-448. [PMID: 31328299 DOI: 10.1111/age.12826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 01/29/2023]
Abstract
Elucidation of the pig microRNAome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits. Here, we extracted small RNAs from skeletal muscle and adipose tissue, and we compared their expression levels between one Western breed (Yorkshire) and seven indigenous Chinese breeds. We detected the expression of 172 known porcine microRNAs (miRNAs) and 181 novel miRNAs. Differential expression analysis found 92 and 12 differentially expressed miRNAs in adipose and muscle tissue respectively. We found that different Chinese breeds shared common directional miRNA expression changes compared to Yorkshire pigs. Some miRNAs differentially expressed across multiple Chinese breeds, including ssc-miR-129-5p, ssc-miR-30 and ssc-miR-150, are involved in adipose tissue function. Functional enrichment analysis revealed that the target genes of the differentially expressed miRNAs are associated mainly with signaling pathways rather than metabolic and biosynthetic processes. The miRNA-target gene and miRNA-phenotypic traits networks identified many hub miRNAs that regulate a large number of target genes or phenotypic traits. Specifically, we found that intramuscular fat content is regulated by the greatest number of miRNAs in muscle tissue. This study provides valuable new candidate miRNAs that will aid in the improvement of meat quality and production.
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Affiliation(s)
- Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - L Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, 610052, Sichuan Province China
| | - Z Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Z He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - R Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - S Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Pang
- Chengdu Biotechservice Institute, Chengdu, 610041, Sichuan Province China
| | - X Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
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Huang J, Zhao J, Zheng Q, Wang S, Wei X, Li F, Shang J, Lei C, Ma Y. Characterization of Circular RNAs in Chinese Buffalo ( Bubalus bubalis) Adipose Tissue: A Focus on Circular RNAs Involved in Fat Deposition. Animals (Basel) 2019; 9:E403. [PMID: 31266200 PMCID: PMC6680660 DOI: 10.3390/ani9070403] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) have been identified as a novel type of regulators involved in multiple biological processes. However, circRNAs with a potential function in fat deposition in buffalo are poorly understood. In this study, six RNA libraries of adipose tissue were constructed for three young and three adult Chinese buffaloes with paired-ends RNA sequencing using the Illumina HiSeq 3000 platform. A total of 5141 circRNAs were computationally identified. Among them, 252 circRNAs were differentially expressed (DE) between the young and adult buffaloes. Of these, 54 were upregulated and 198 were downregulated in the adult group. Eight DE circRNAs were further identified by quantitative real-time-PCR (qRT-PCR) and Sanger sequencing. Co-expression analysis revealed that 34 circRNAs demonstrated a strong correlation with fat deposition-associated genes (|r| > 0.980). Among these, expressional correlation between two circRNAs (19:45387150|45389986 and 21:6969877|69753491) and PR/SET domain 16 was further verified using qRT-PCR, and a strong correlation was revealed (1 > |r| > 0.8). These results strongly suggest that circRNAs 19:45387150|45389986 and 21:6969877|69753491 are potential regulators of buffalo fat deposition. In summary, this study characterized the circRNA profiles of adipose tissues at different stages for the first time and revealed two circRNAs strongly correlated with fat deposition-associated genes, which provided new candidate regulators for fat deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China
| | - Jinhui Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Qiuzhi Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Shuzhe Wang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Jianghua Shang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China.
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China.
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23
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Liu X, Wei S, Deng S, Li D, Liu K, Shan B, Shao Y, Wei W, Chen J, Zhang L. Genome-wide identification and comparison of mRNAs, lncRNAs and circRNAs in porcine intramuscular, subcutaneous, retroperitoneal and mesenteric adipose tissues. Anim Genet 2019; 50:228-241. [PMID: 30982992 DOI: 10.1111/age.12781] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 01/31/2023]
Abstract
Many types of RNAs, including messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), play crucial roles in regulating fat cell differentiation and tissue development. However, the expression profiles of these RNAs in different adipose tissues are still largely unknown. To shed light on this issue, we performed a transcriptome analysis of mRNAs, lncRNAs and circRNAs obtained from intramuscular adipose tissue, subcutaneous adipose tissue, retroperitoneal adipose tissue and mesenteric adipose tissue of Chinese Erhualian pigs. A number of differentially expressed mRNAs, lncRNAs and circRNAs were identified among the four adipose tissues. Tissue-specific analysis indicated that circRNAs exhibited the highest tissue specificity among mRNAs, lncRNAs and circRNAs, whereas intramuscular adipose tissue had the most tissue-specific genes among the four adipose tissues. Gene Ontology analysis showed that differentially expressed mRNAs among groups were involved mainly in lipid metabolism and immune inflammatory response processes. Furthermore, the co-expression network construction of mRNAs-lncRNAs revealed that several important lncRNAs, such as MSTRG.426159 and MSTRG.604206, might associate with lipid metabolic process. Taken together, these data provide a genome-wide resource of mRNAs, lncRNAs and circRNAs potentially involved in porcine fat metabolism, thus improving understanding of their function in diverse adipose tissues.
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Affiliation(s)
- X Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - S Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - S Deng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - D Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - K Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - B Shan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Y Shao
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China
| | - W Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - J Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - L Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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Bao X, He X, Zheng S, Sun J, Luo Y, Tan R, Zhao J, Zhong F, Zhang L. Up-regulation of circular RNA hsa_circ_0037909 promotes essential hypertension. J Clin Lab Anal 2019; 33:e22853. [PMID: 30861600 PMCID: PMC6528570 DOI: 10.1002/jcla.22853] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/24/2023] Open
Abstract
Aims Essential hypertension (EH) is a high prevalence disease facing a public health challenge. People were little known about the genetics of diagnosing the cause of EH. Circular RNAs that have a continuous cycle of covalent closure, without affected by RNA exonuclease, and are more stable and hard to degrade may involve into the molecule regulation mechanism of EH as an important biomedical. Methods qRT‐PCR was used to analyze circRNAs in total volume of human blood and the induced human aortic endothelial cells (HAECs) and human umbilical vein endothelial cells (HUVECs). Our case‐control study was involved with 48 pairs of case controls with sex and age (±3 years) match. We conducted t test, Pearson's χ2 test, and receiver operating characteristics (ROC) curve analysis for the corresponding analysis. Results The expression level of hsa_circ_0037909 in EH patients was significantly higher than that in the healthy controls (P = 0.007), and the expression level of hsa‐miR‐637 in EH patients was significantly lower in than that in the healthy controls (P = 0.039); the same result appears in the HAECs and HUVECs. Hsa‐miR‐637 (adjusted P = 0.018), hsa_circ_0037909 (adjusted P = 0.005), HDL (adjusted P = 0.024), and serum creatinine (adjusted P = 0.014) were brought into the model which performed logistic regression analysis. The combination of two RNAs was excellent (P < 0.001) through ROC curve analysis. Hsa_circ_0037909 was significantly positively correlated with serum creatinine (P < 0.001) and low‐density lipoprotein (LDL) (P = 0.017). Conclusions Our findings suggested that the combination of hsa_circ_0037911 and hsa‐miR‐637 may be a significant important biomarker for early diagnosis of EH. Hsa_circ_0037909 may affect serum creatinine or LDL leading to the formation of EH.
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Affiliation(s)
- Xingjie Bao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Xin He
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Shuying Zheng
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Jihan Sun
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Yizhe Luo
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Ronghui Tan
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Jinshun Zhao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
| | - Fade Zhong
- Ningbo Municipal Blood Center, Ningbo, China
| | - Lina Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, China
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25
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Cao Y, You S, Yao Y, Liu ZJ, Hazi W, Li CY, Zhang XY, Hou XX, Wei JC, Li XY, Wang DW, Chen CF, Zhang YF, Ni W, Hu SW. Expression profiles of circular RNAs in sheep skeletal muscle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1550-1557. [PMID: 29642686 PMCID: PMC6127590 DOI: 10.5713/ajas.17.0563] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/13/2018] [Indexed: 12/20/2022]
Abstract
Objective Circular RNAs (circRNAs) are a newfound class of non-coding RNA in animals and plants. Recent studies have revealed that circRNAs play important roles in cell proliferation, differentiation, autophagy and apoptosis during development. However, there are few reports about muscle development-related circRNAs in livestock. Methods RNA sequencing analysis was employed to identify and annotate circRNAs from longissimus dorsi of sheep. Reverse transcription followed by real-time quantitative (q) polymerase chain reaction (PCR) analysis verified the presence of these circRNAs. Targetscan7.0 and miRanda were used to analyse the interaction of circRNA-microRNA (miRNA). To investigate the function of circRNAs, an experiment was conducted to perform enrichment analysis hosting genes of circRNAs using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Results About 75.5 million sequences were obtained from RNA libraries of sheep skeletal muscle. These sequences were mapped to 729 genes in the sheep reference genome. We identified 886 circRNAs, including numerous circular intronic RNAs and exonic circRNAs. Reverse transcription PCR (RT-PCR) and DNA sequencing analysis confirmed the presence of several circRNAs. Real-Time RT-PCR analysis exhibited resistance of sheep circRNAs to RNase R digestion. We found that many circRNAs interacted with muscle-specific miRNAs involved in growth and development of muscle, especially circ776. The GO and KEGG enrichment analysis showed that hosting genes of circRNAs was involved in muscle cell development and signaling pathway. Conclusion The study provides comprehensive expression profiles of circRNAs in sheep skeletal muscle. Our study offers a large number of circRNAs to facilitate a better understanding of their roles in muscle growth. Meanwhile, we suggested that circ776 could be analyzed in future study.
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Affiliation(s)
- Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shuang You
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhi-Jin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Cun-Yuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiang-Yu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiao-Xu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jun-Chang Wei
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiao-Yue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Da-Wei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Chuang-Fu Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yun-Feng Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Sheng-Wei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
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Li C, Li X, Yao Y, Ma Q, Ni W, Zhang X, Cao Y, Hazi W, Wang D, Quan R, Hou X, Liu Z, Zhan Q, Liu L, Zhang M, Yu S, Hu S. Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep. Oncotarget 2017; 8:97165-97177. [PMID: 29228601 PMCID: PMC5722553 DOI: 10.18632/oncotarget.21835] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep. A total of 6113 circRNAs were detected from the RNA-seq data. Several circRNAs were identified using reverse transcription PCR, DNA sequencing and RNase R digestion experiments. The expression levels of several circRNAs in prenatal and postnatal muscle were confirmed by Real-Time RT-PCR. The gene ontology (GO) and KEGG enrichment analysis of the host gene of the circRNAs showed that these circRNAs were mainly involved in the growth and development of muscle related signaling pathways. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. The circRNAs expression profiles in muscle provided an important reference for the study of circRNAs in sheep.
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Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qiman Ma
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qianqian Zhan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
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