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Li X, Hou Z, Meng S, Jia Q, Xing S, Wang Z, Chen M, Xu H, Li M, Cai H. LncRNA BlncAD1 Modulates Bovine Adipogenesis by Binding to MYH10, PI3K/Akt Signaling Pathway, and miR-27a-5p/CDK6 Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11094-11110. [PMID: 38661523 DOI: 10.1021/acs.jafc.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Research on adipogenesis will help to improve the meat quality of livestock. Long noncoding RNAs (lncRNAs) are involved in mammalian adipogenesis as epigenetic modulators. In this study, we analyzed lncRNA expression during bovine adipogenesis and detected 195 differentially expressed lncRNAs, including lncRNA BlncAD1, which was significantly upregulated in mature bovine adipocytes. Gain- and loss-of-function experiments confirmed that BlncAD1 promoted the proliferation, apoptosis, and differentiation of bovine preadipocytes. RNA pull-down revealed that the nonmuscle myosin 10 (MYH10) is a potential binding protein of BlncAD1. Then, we elucidated that loss of BlncAD1 caused increased ubiquitination of MYH10, which confirmed that BlncAD1 regulates adipogenesis by enhancing the stability of the MYH10 protein. Western blotting was used to demonstrate that BlncAD1 activated the PI3K/Akt signaling pathway. Bioinformatic analysis and dual-luciferase reporter assays indicated that BlncAD1 competitively absorbed miR-27a-5p. The overexpression and interference of miR-27a-5p in bovine preadipocytes displayed that miR-27a-5p inhibited proliferation, apoptosis, and differentiation. Further results suggested that miR-27a-5p targeted the CDK6 gene and that BlncAD1 controlled the proliferation of bovine preadipocytes by modulating the miR-27a-5p/CDK6 axis. This study revealed the complex mechanisms of BlncAD1 underlying bovine adipogenesis for the first time, which would provide useful information for genetics and breeding improvement of Chinese beef cattle.
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Affiliation(s)
- Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongyi Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shengbo Meng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shanshan Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhitong Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjuan Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Dong X, Cheng Y, Qiao L, Wang X, Zeng C, Feng Y. Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1. Genes (Basel) 2021; 12:1325. [PMID: 34573307 PMCID: PMC8470131 DOI: 10.3390/genes12091325] [Citation(s) in RCA: 3] [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: 07/07/2021] [Accepted: 08/25/2021] [Indexed: 02/02/2023] Open
Abstract
Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.
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Affiliation(s)
| | | | | | | | | | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (Y.C.); (L.Q.); (X.W.); (C.Z.)
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Zhang P, Du J, Guo X, Wu S, He J, Li X, Shen L, Chen L, Li B, Zhang J, Xie Y, Niu L, Jiang D, Li X, Zhang S, Zhu L. LncMyoD Promotes Skeletal Myogenesis and Regulates Skeletal Muscle Fiber-Type Composition by Sponging miR-370-3p. Genes (Basel) 2021; 12:genes12040589. [PMID: 33920575 PMCID: PMC8072939 DOI: 10.3390/genes12040589] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
The development of skeletal muscle is a highly ordered and complex biological process. Increasing evidence has shown that noncoding RNAs, especially long-noncoding RNAs (lncRNAs) and microRNAs, play a vital role in the development of myogenic processes. In this study, we observed that lncMyoD regulates myogenesis and changes myofiber-type composition. miR-370-3p, which is directly targeted by lncMyoD, promoted myoblast proliferation and inhibited myoblast differentiation in the C2C12 cell line, which serves as a valuable model for studying muscle development. In addition, the inhibition of miR-370-3p promoted fast-twitch fiber transition. Further analysis indicated that acyl-Coenzyme A dehydrogenase, short/branched chain (ACADSB) is a target gene of miR-370-3p, which is also involved in myoblast differentiation and fiber-type transition. Furthermore, our data suggested that miR-370-3p was sponged by lncMyoD. In contrast with miR-370-3p, lncMyoD promoted fast-twitch fiber transition. Taken together, our results suggest that miR-370-3p regulates myoblast differentiation and muscle fiber transition and is sponged by lncMyoD.
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Affiliation(s)
- Peiwen Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingjing Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinyu Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuang Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinrong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Bohong Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
| | - Jingjun Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
| | - Yuhao Xie
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Dongmei Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.Z.); (J.D.); (X.G.); (S.W.); (J.H.); (X.L.); (L.S.); (L.C.); (B.L.); (J.Z.); (Y.X.); (L.N.); (D.J.); (X.L.); (S.Z.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence:
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Sun K, Wang H, Sun H. NAMS webserver: coding potential assessment and functional annotation of plant transcripts. Brief Bioinform 2020; 22:5906158. [PMID: 33080021 PMCID: PMC8138890 DOI: 10.1093/bib/bbaa200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/23/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
Recent advances in transcriptomics have uncovered lots of novel transcripts in plants. To annotate such transcripts, dissecting their coding potential is a critical step. Computational approaches have been proven fruitful in this task; however, most current tools are designed/optimized for mammals and only a few of them have been tested on a limited number of plant species. In this work, we present NAMS webserver, which contains a novel coding potential classifier, NAMS, specifically optimized for plants. We have evaluated the performance of NAMS using a comprehensive dataset containing more than 3 million transcripts from various plant species, where NAMS demonstrates high accuracy and remarkable performance improvements over state-of-the-art software. Moreover, our webserver also furnishes functional annotations, aiming to provide users informative clues to the functions of their transcripts. Considering that most plant species are poorly characterized, our NAMS webserver could serve as a valuable resource to facilitate the transcriptomic studies. The webserver with testing dataset is freely available at http://sunlab.cpy.cuhk.edu.hk/NAMS/.
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Affiliation(s)
- Kun Sun
- Corresponding authors: Kun Sun, Shenzhen Bay Laboratory, Shenzhen 518132, China. Tel.: +86-0755-2641-9310; Fax: +86-755-8696-7710. E-mail: ; Hao Sun, Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR 999077, China. Tel.: +852-3763-6048; Fax: +852-2636-5090. E-mail:
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5
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Identification of key HIF-1α target genes that regulate adaptation to hypoxic conditions in Tibetan chicken embryos. Gene 2020; 729:144321. [DOI: 10.1016/j.gene.2019.144321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 12/21/2019] [Indexed: 12/11/2022]
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Chen L, Guo T, Yu Y, Sun Y, Yu G, Cheng L. Heat shock cognate protein 70 promotes the differentiation of C2C12 myoblast and targets Yin Yang 1. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:551. [PMID: 31807532 DOI: 10.21037/atm.2019.09.88] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Heat shock cognate protein 70 (HSC70) is a constitutively expressed molecular chaperone protein which can maintain the structure and function of the protein. HSC70 is engaged in a variety of physiological processes, yet its role during skeletal muscle differentiation is still unclear. Methods C2C12 cells were obtained and cultured. During differentiation, the expression of HSC70 was evaluated by RT-PCR. To determine the function of HSC70 during C2C12 myoblast differentiation, myotube transfection of siR-HSC70 was performed with Lipofectamine 2000 Reagent. Western blot was used to measure the expression of Yin Yang 1 (YY1) after down-regulating HSC70. To further assess if YY1 mediates the pro-differentiation effect of HSC70, a plasmid of YY1 overexpression was used to increase the expression of YY1 in the presence of siR-HSC70-2. The formation of myotubes was visualized by immunofluorescent staining, while the expression levels of MyoD and MyoG were evaluated by RT-PCR. Results In this study, we found that HSC70 was up-regulated during C2C12 myoblast differentiation. Knockdown of HSC70 not only inhibited the C2C12 myoblast differentiation but also reduced the expression of MyoD and MyoG. When YY1 protein was over-expressed, it could restore the differentiation in cells with HSC70 knockdown or inhibition. Conclusions Collectively, this study demonstrates that HSC70 is involved in the regulation of C2C12 myoblast differentiation via YY1 and may serve as a potential target for a therapeutic strategy to prevent muscle atrophy.
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Affiliation(s)
- Lei Chen
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Tao Guo
- Department of Orthopedics, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Yan Yu
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Yeqing Sun
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Guangrong Yu
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
| | - Liming Cheng
- Department of Orthopedics, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Ministry of Education of the People's Republic of China, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai 200065, China
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7
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Wang S, Zuo H, Jin J, Lv W, Xu Z, Fan Y, Zhang J, Zuo B. Long noncoding RNA Neat1 modulates myogenesis by recruiting Ezh2. Cell Death Dis 2019; 10:505. [PMID: 31243262 PMCID: PMC6594961 DOI: 10.1038/s41419-019-1742-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/02/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022]
Abstract
Neat1 is widely expressed in many tissues and cells and exerts pro-proliferation effects on many cancer cells. However, little is known about the function of Neat1 in myogenesis. Here we characterized the roles of Neat1 in muscle cell formation and muscle regeneration. Gain- or loss-of-function studies in C2C12 cells demonstrated that Neat1 accelerates myoblast proliferation but suppresses myoblast differentiation and fusion. Further, knockdown of Neat1 in vivo increased the cross-sectional area of muscle fibers but impaired muscle regeneration. Mechanically, Neat1 physically interacted with Ezh2 mainly through the core binding region (1001–1540 bp) and recruited Ezh2 to target gene promoters. Neat1 promoted myoblast proliferation mainly by decreasing the expression of the cyclin-dependent kinase inhibitor P21 gene but inhibited myoblast differentiation by suppressing the transcription of myogenic marker genes, such as Myog, Myh4, and Tnni2. Altogether, we uncover a previously unknown function of Neat1 in muscle development and the molecular mechanism by which Neat1 regulates myogenesis.
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Affiliation(s)
- Shanshan Wang
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Hao Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Jianjun Jin
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Wei Lv
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Yonghui Fan
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Jiali Zhang
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China.,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China. .,Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, Hubei, People's Republic of China. .,The Cooperative Innovation Center for Sustainable Pig Production, 430070, Wuhan, People's Republic of China.
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Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. Genes (Basel) 2018; 9:genes9010034. [PMID: 29324704 PMCID: PMC5793186 DOI: 10.3390/genes9010034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/22/2022] Open
Abstract
A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships. In addition, Pearson’s correlation coefficients demonstrated that 990 lncRNAs and 7436 mRNAs were possibly in trans-regulatory relationships. These co-expressed mRNAs were enriched in various developmentally-related biological processes, such as myocyte proliferation and differentiation, myoblast differentiation, and myoblast fusion. The number of transcripts (906 lncRNAs and 4422 mRNAs) differentially expressed across various stages declined with the progression of differentiation. Then, 4422 differentially expressed genes were assigned to four clusters according to K-means analysis. Genes in the K1 cluster likely play important roles in myoblast proliferation and those in the K4 cluster were likely associated with the initiation of myoblast differentiation, while genes in the K2 and K3 clusters were likely related to myoblast fusion. This study provides a catalog of chicken lncRNAs and mRNAs for further experimental investigations and facilitates a better understanding of skeletal muscle development.
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