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Integrated analysis of miRNA and mRNA transcriptomic reveals antler growth regulatory network. Mol Genet Genomics 2021; 296:689-703. [PMID: 33770271 DOI: 10.1007/s00438-021-01776-z] [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: 01/30/2021] [Accepted: 03/15/2021] [Indexed: 01/26/2023]
Abstract
The growth of antler is driven by endochondral ossification in the growth center of the apical region. Antler grows faster than cancer tissues, but it can be stably regulated and regenerated periodically. To elucidate the molecular mechanisms of how antler grows rapidly without carcinogenesis, in this study, we used RNA-seq technology to evaluate the changes of miRNA and mRNA profiles in antler at four different developmental stages, including 15, 60, 90, and 110 days. We identified a total of 55004 unigenes and 246 miRNAs of which, 10182, 13258, 10740 differentially expressed (DE) unigenes and 35, 53, 27 DE miRNAs were identified in 60-day vs. 15-day, 90-day vs. 60-day, and 110-day vs. 90-day. GO and KEGG pathway analysis indicated that DE unigenes and DE miRNA were mainly associated with chondrogenesis, osteogenesis and inhibition of oncogenesis, that were closely related to antler growth. The interaction networks of mRNA-mRNA and miRNA-mRNA related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler were constructed. The results indicated that mRNAs (COL2A1, SOX9, WWP2, FGFR1, SPARC, LOX, etc.) and miRNAs (miR-145, miR-199a-3p, miR-140, miR-199a-5p, etc.) might have key roles in chondrogenesis and osteogenesis of antler. As well as mRNA (TP53, Tpm3 and ATP1A1, etc.) and miRNA (miR-106a, miR-145, miR-1260b and miR-2898, etc.) might play important roles in inhibiting the carcinogenesis of antler. In summary, we constructed the mRNA-mRNA and miRNA-mRNA regulatory networks related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler, and identified key candidate mRNAs and miRNAs among them. Further developments and validations may provide a reference for in-depth analysis of the molecular mechanism of antler growth without carcinogenesis.
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Chen DY, Jiang RF, Li YJ, Liu MX, Wu L, Hu W. Screening and functional identification of lncRNAs in antler mesenchymal and cartilage tissues using high-throughput sequencing. Sci Rep 2020; 10:9492. [PMID: 32528134 PMCID: PMC7289821 DOI: 10.1038/s41598-020-66383-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNA (lncRNA) is a transcription product of the mammalian genome that regulates the development and growth in the body. The present study aimed to analyze the expression dynamics of lncRNA in sika antler mesenchymal and cartilage tissues by high-throughput sequencing. Bioinformatics was applied to predict differentially expressed lncRNAs and target genes and screen lncRNAs and mRNAs related to osteogenic differentiation, cell proliferation, and migration. Finally, the expression of the lncRNAs and target genes were analyzed by qRT-PCR. The results showed that compared to the cartilage tissue, the transcription levels of lncRNA and mRNA, 1212 lncRNAs and 518 mRNAs, in mesenchymal tissue were altered significantly. Thus, a complex interaction network was constructed, and the lncRNA-mRNA interaction network correlation related to osteogenic differentiation, cell proliferation, and migration was analyzed. Among these, the 26 lncRNAs and potential target genes were verified by qRT-PCR, and the results of qRT-PCR were consistent with high-throughput sequencing results. These data indicated that lncRNA promotes the differentiation of deer antler mesenchymal tissue into cartilage tissue by regulating the related osteogenic factors, cell proliferation, and migration-related genes and accelerating the process of deer antler regeneration and development.
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Affiliation(s)
- Dan-Yang Chen
- College of Life Science, Jilin Agriculture University, Changchun, Jilin Province, 130118, China
| | - Ren-Feng Jiang
- College of Life Science, Jilin Agriculture University, Changchun, Jilin Province, 130118, China
| | - Yan-Jun Li
- College of Life Science, Jilin Agriculture University, Changchun, Jilin Province, 130118, China
| | - Ming-Xiao Liu
- College of Life Science, Jilin Agriculture University, Changchun, Jilin Province, 130118, China
| | - Lei Wu
- College of Life Science, Jilin Agriculture University, Changchun, Jilin Province, 130118, China.
| | - Wei Hu
- College of Life Science, Jilin Agriculture University, Changchun, Jilin Province, 130118, China.
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Yan Y, Chen D, Han X, Liu M, Hu W. MiRNA-19a and miRNA-19b regulate proliferation of antler cells by targeting TGFBR2. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00469-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Liu M, Han X, Cui D, Yan Y, Li L, Hu W. Post-transcriptional regulation of miRNA-15a and miRNA-15b on VEGFR gene and deer antler cell proliferation. ACTA ACUST UNITED AC 2019. [DOI: 10.1515/tjb-2018-0160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
Background
Deer antler is the only regenerative organ in mammals, the regeneration of antler is not only the regeneration of bone tissue, but also accompanied by the regeneration of nerves, blood vessels and so on. The purpose of the current study was to explore the effect of miRNA-15a and miRNA-15b on the regulation of sika deer vascular endothelial growth factor receptor (VEGFR) during rapid antler growth.
Materials and methods
The VEGFR 3′-UTR was analyzed by bioinformatics software to identify the highly matched miRNAs. After transfected with miRNA mimics, the expression of selected miRNAs were measured by RT-qPCR and the relative expression level of VEGFR protein was detected by Western Blot. Dual-luciferase activity assay was used to determine the target relationship between VEGFR and miRNAs. The cartilage cell proliferation and telomerase activity were measured by MTT kit and TRAP assay, respectively.
Results
The VEGFR 3′-UTR contains a binding site for miRNA-15a and miRNA-15b. Over-expression of miRNA-15a and miRNA-15b, which significantly reduced the expression level of VEGFR protein, inhibited the proliferation of cartilage cells, and decreased the telomerase activity of cartilage cells in vitro.
Conclusion
miRNA-15a and miRNA-15b represent novel regulatory factors of VEGFR expression in deer antler.
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Yao B, Zhang M, Liu M, Lu B, Leng X, Hu Y, Zhao D, Zhao YU. Identification of the miRNA-mRNA regulatory network of antler growth centers. J Biosci 2019; 44:11. [PMID: 30837362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Antler growth is a unique event compared to other growth and development processes in mammals. Antlers grow extremely fast during the rapid growth stage when growth rate peaks at 2 cm per day. Antler growth is driven by a specific endochondral ossification process in the growth center that is in the distal region of the antler tip. In this study, we used state-of-art RNA-seq technology to analyze the expression profiles of mRNAs and miRNAs during antler growth. Our results indicated that the expression levels of multiple genes involved in chondrogenesis and endochondral ossification, including Fn1, Sox9, Col2a1, Acan, Col9a1, Col11a1, Hapln1, Wwp2, Fgfr3, Comp, Sp7 and Ihh, were significantly increased at the rapid growth stage. Our results also indicated that there were multiple differentially expressed miRNAs interacting with differentially expressed genes with opposite expression patterns. Furthermore, some of the miRNAs, including miR-3072-5p, miR-1600, miR-34-5p, miR-6889-5p and miR-6729-5p, simultaneously interacted with and controlled multiple genes involved in the process of chondrogenesis and endochondral ossification. Therefore, we established a miRNA-mRNA regulatory network by identifying miRNAs and their target genes that were differentially expressed in the antler growth centers by comparing the rapid growth stage and the initial growth stage.
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Affiliation(s)
- Baojin Yao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
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Liu J, Ning C, Li B, Li R, Wu W, Liu H. Transcriptome comparison between prenatal and postnatal Large White livers identifies differences in the expression level of genes related to metabolism and postnatal growth. Gene 2018; 686:92-103. [PMID: 30321659 DOI: 10.1016/j.gene.2018.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/06/2018] [Accepted: 10/11/2018] [Indexed: 11/16/2022]
Abstract
The current study examined the liver transcriptomic profiles of the Large White different in developmental periods. It was performed on pigs of two developmental stages: 70-day fetus (P70) and 70-day piglets (D70). The objective of the study was to identify genes associated with Large White liver lipid metabolism, growth and development. We sequenced eight sRNA libraries of liver samples from four Large White at P70 and D70 respectively. We totally obtained 19,202 genes. 4916 of them were found to be differentially expressed (DEGs) (p < 0.05, fold change ≥ 1), of which 2502 were up-regulated and 2414 were down-regulated. GO enrichment and KEGG pathway analysis indicated that ACACA, ACADM, ACAA2 and HADH were simultaneously enriched in diverse pathways related to lipid metabolism, and so they were considered to be the promising candidate genes which could affect the porcine liver lipid metabolism. Notably, the gene insulin-like growth factor 1 (IGF1) which participated in somatotropic axis signaling was found to be up-regulated in D70 compared with P70. miRWalk and TargetScan softwares were used to screen the miRNAs which bound to the 3' untranslated region (3'UTR) of IGF1. After integration analysis with miRNAs sequencing data, miR-18b and miR-130b-3p were selected for further study. MiR-18b and miR-130b-3p were down-regulated in D70 compared with P70. Dual luciferase assays indicated that miR-18b and miR-130b-3p could obviously decrease (p < 0.05) the fluorescence activity of the group transfected with the wild-type vector of IGF1 3'UTR, while the relative luciferase activity of the group transfected with the mutant vector of IGF1 3'UTR did not change significantly. Taken together, it indicated that miR-18b and miR-130b-3p could target IGF1 directly.
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Affiliation(s)
- Jingge Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 21009, PR China
| | - Caibo Ning
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 21009, PR China.
| | - Bojiang Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 21009, PR China
| | - Rongyang Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 21009, PR China
| | - Wangjun Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 21009, PR China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 21009, PR China.
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Yao B, Zhang M, Liu M, Wang Q, Liu M, Zhao Y. Sox9 Functions as a Master Regulator of Antler Growth by Controlling Multiple Cell Lineages. DNA Cell Biol 2018; 37:15-22. [DOI: 10.1089/dna.2017.3885] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Baojin Yao
- Chinese Medicine and Bioengineering Research and Development Center, Changchun University of Chinese Medicine, Changchun, China
| | - Mei Zhang
- Innovation Practice Center, Changchun University of Chinese Medicine, Changchun, China
| | - Meichen Liu
- Chinese Medicine and Bioengineering Research and Development Center, Changchun University of Chinese Medicine, Changchun, China
| | - Qun Wang
- Chinese Medicine and Bioengineering Research and Development Center, Changchun University of Chinese Medicine, Changchun, China
| | - Meixin Liu
- Chinese Medicine and Bioengineering Research and Development Center, Changchun University of Chinese Medicine, Changchun, China
| | - Yu Zhao
- Chinese Medicine and Bioengineering Research and Development Center, Changchun University of Chinese Medicine, Changchun, China
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Yang JJ, Tao H, Liu LP, Hu W, Deng ZY, Li J. miR-200a controls hepatic stellate cell activation and fibrosis via SIRT1/Notch1 signal pathway. Inflamm Res 2016; 66:341-352. [PMID: 28025657 DOI: 10.1007/s00011-016-1020-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 12/06/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES miR-200a has been established as a key regulator of HSC activation processes in liver fibrosis. Epigenetic silencing of miR-200a contributing to SIRT1 over-expression has been discussed in breast cancer; however, whether miR-200a controls SIRT1 gene expression in hepatic fibrosis is still unknown. METHODS AND MATERIALS We analyzed miR-200a regulation of SIRT1 expression in CCl4-induced liver fibrosis and TGF-β1-mediated activation of HSC. miR-200a, SIRT1, α-SMA, Col1A1, Notch1 and NICD expression were estimated by Western blotting, qRT-PCR and Immunohistochemistry. HSCs were transfected with miR-200a mimic, miR-200a inhibitor and SIRT1-RNAi. Luciferase reporter assays further confirmed the interaction between miR-200a and the SIRT1 mRNA 3'-UTR. Cell proliferation ability was assessed by MTT and cell cycle. RESULTS We found that treatment activated HSC with miR-200a mimics, restored miR-200a expression and reduced SIRT1 levels. Conversely, treatment activated HSC with miR-200a inhibitors, decreased miR-200a expression and up-regulated SIRT1 levels. Restoration of miR-200a or the knockdown of SIRT1 prevented HSC activation and proliferation. We have established the SIRT1 transcript as subject to regulation by miR-200a, through miR-200a targeting of SIRT1 3'-UTR. Finally, HSC transfected with SIRT1-siRNA increased the levels of Notch1 protein and mRNA expression. CONCLUSIONS Our study demonstrated that miR-200a regulates SIRT1/Notch1 expression during HSC activation and fibrosis.
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Affiliation(s)
- Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Li-Ping Liu
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Wei Hu
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Zi-Yu Deng
- Department of Scientific, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Mei Shan Road, Hefei, Anhui, 230032, China.
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Tao H, Chen ZW, Yang JJ, Shi KH. MicroRNA-29a suppresses cardiac fibroblasts proliferation via targeting VEGF-A/MAPK signal pathway. Int J Biol Macromol 2016; 88:414-23. [PMID: 27060017 DOI: 10.1016/j.ijbiomac.2016.04.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/18/2016] [Accepted: 04/04/2016] [Indexed: 10/25/2022]
Abstract
Cardiac fibroblasts proliferation is the most important pathophysiological character of cardiac fibrosis while the underlying mechanisms are still incompletely known. MicroRNAs (miRNAs) regulate gene expression by binding to specific sites. Studies have been indicated that miRNA-29a play a key role in cardiac fibrosis. VEGF-A carries out its functions through MAPK signaling pathway in cardiac fibrosis. Existing proofs predict that the VEGF-A is one of the potential targets of miRNA-29a. We therefore probe the role of miRNA-29a and its latent target VEGF-A during cardiac fibrosis. In our study, miRNA-29a was down-regulated while VEGF-A was up-regulated in cardiac fibrosis tissues. The rat cardiac fibroblasts that were transfected with miRNA-29a inhibitor exhibited low-expression of miRNA-29a, enhanced VEGF-A protein and mRNA expression. Nevertheless, the cardiac fibroblasts transfected with miRNA-29a mimics obtained the opposite expression result. Furthermore, over-expression of miRNA-29a suppresses cardiac fibroblasts proliferation. In conclusion, these results suggested that miRNA-29a suppresses cardiac fibrosis and fibroblasts proliferation via targeting VEGF-A/MAPK signal pathway implicating that miRNA-29a might play a role in the treatment of cardiac fibrosis.
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Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China; Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China
| | - Ze-Wen Chen
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China; Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China; Cardiovascular Research Center, Anhui Medical University, Hefei 230601, China.
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