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Li CC, Hu R, Hua XM, Ni YX, Ge L, Zhang L, Yu W, Hao NX, Xia H, Fang Q, Tao ZY. Construction and functional verification of size-reduced plasmids based on TMP resistance gene dfrB10. Microbiol Spectr 2023; 11:e0120623. [PMID: 37905802 PMCID: PMC10714783 DOI: 10.1128/spectrum.01206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Plasmid size is one of the factors affecting transfection efficacy in most of the molecular genetic research studies. One effective approach for reducing plasmid size is to replace relatively large, conventional antibiotic resistance genes with the short-size dfrB10 gene. The successful construct of a series of dfrB10-based tool plasmids and their functional validation, via comparison with original plasmids, suggest that dfrB10 is a potent drug resistance selection marker. The antibiotic trimethoprim offers convenient usage comparable to that of ampicillin or kanamycin. Additionally, fluorescence analysis has demonstrated the compatibility of TMP with protein expression in various host cells. Based on these findings, TMP-dfrB10 could be an alternative choice for future use in molecular genetic research studies that require miniature plasmids to achieve optimal results.
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Affiliation(s)
- Chun-cao Li
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Rui Hu
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Xiu-min Hua
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Yi-xuan Ni
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Lu Ge
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Lu Zhang
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Wen Yu
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Ni-xin Hao
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Hui Xia
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Qiang Fang
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
| | - Zhi-yong Tao
- Department of Microbiology and Parasitology, Bengbu Medical College, Bengbu, Anhui, China
- Anhui Key Laboratory of Infection and Immunology, Bengbu Medical College, Bengbu, Anhui, China
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Yu M, He X, Liu T, Li J. lncRNA GPRC5D-AS1 as a ceRNA inhibits skeletal muscle aging by regulating miR-520d-5p. Aging (Albany NY) 2023; 15:13980-13997. [PMID: 38100482 PMCID: PMC10756129 DOI: 10.18632/aging.205279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 10/23/2023] [Indexed: 12/17/2023]
Abstract
Sarcopenia induced by muscle aging is associated with negative outcomes in a variety of diseases. Long non-coding RNAs are a class of RNAs longer than 200 nucleotides with lower protein coding potential. An increasing number of studies have shown that lncRNAs play a vital role in skeletal muscle development. According to our previous research, lncRNA GPRC5D-AS1 is selected in the present study as the target gene to further study its effect on skeletal muscle aging in a dexamethasone-induced human muscle atrophy cell model. As a result, GPRC5D-AS1 functions as a ceRNA of miR-520d-5p to repress cell apoptosis and regulate the expression of muscle regulatory factors, including MyoD, MyoG, Mef2c and Myf5, thus accelerating myoblast proliferation and differentiation, facilitating development of skeletal muscle. In conclusion, lncRNA GPRC5D-AS1 could be a novel therapeutic target for treating sarcopenia.
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Affiliation(s)
- Miao Yu
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiuting He
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| | - Ting Liu
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
| | - Jie Li
- Department of Geriatrics and Special Medical Treatment, The First Hospital of Jilin University, Changchun 130021, China
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Liu Q, Li M, Xie S, Tian C, Li J, Wang Y, Li X, Li C. MYOD induced lnc-MEG3 promotes porcine satellite cell differentiation via interacting with DLST. Epigenetics 2023; 18:2237789. [PMID: 37506369 PMCID: PMC10392761 DOI: 10.1080/15592294.2023.2237789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 07/30/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in the process of muscle cell differentiation and play an important role. Previous studies have shown that lncRNA-MEG3 promotes the differentiation of porcine skeletal muscle satellite cells (PSCs), but the regulatory mechanism of MEG3 interaction with target protein has not been well studied. We demonstrated that MEG3 can bind dihydrolipoamide succinyltransferase (DLST) by RNA pull down and RIP-qPCR. Subsequently, knockdown and overexpression experiments showed that DLST promotes PSCs differentiation. Rescue experiments showed that the expression of DLST protein was significantly increased with MEG3 overexpression and decreased with MEG3 knockdown, while its mRNA expression was not changed. Furthermore, we have successfully predicted and validated that the transcription factor myogenic differentiation (MYOD) binds to the MEG3 core promoter though utilizing chromatin immunoprecipitation (CHIP) and luciferase reporter assays. The results indicated that MYOD acts as a transcription factor of MEG3 to promote MEG3 transcription. Knockdown of MEG3 in vivo indicated that MEG3 is involved in skeletal muscle regeneration. It is concluded that MYOD acts as a transcription factor to induce MEG3 expression. MEG3 acts as a molecular scaffold to bind and promote DLST protein expression. This paper provides a new molecular mechanism for MEG3 to promote the differentiation of PSCs.
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Affiliation(s)
- Quan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
- Guangxi Guigang Super Gene Technology Co. Ltd, Guigang, Guangxi, P. R. China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Su Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Cheng Tian
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Jiaxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Xin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
- Guangxi Guigang Super Gene Technology Co. Ltd, Guigang, Guangxi, P. R. China
- The Cooperative Innovation Center for Sustainable Pig Production of Hubei Province, Wuhan, Hubei, P. R. China
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Li J, Chen C, Zhao R, Wu J, Li Z. Transcriptome analysis of mRNAs, lncRNAs, and miRNAs in the skeletal muscle of Tibetan chickens at different developmental stages. Front Physiol 2023; 14:1225349. [PMID: 37565148 PMCID: PMC10410567 DOI: 10.3389/fphys.2023.1225349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/12/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction: As a valuable genetic resource, native birds can contribute to the sustainable development of animal production. Tibetan chickens, known for their special flavor, are one of the important local poultry breeds in the Qinghai-Tibet Plateau. However, Tibetan chickens have a slow growth rate and poor carcass traits compared with broilers. Although most of the research on Tibetan chickens focused on their hypoxic adaptation, there were fewer studies related to skeletal muscle development. Methods: Here, we performed the transcriptional sequencing of leg muscles from Tibetan chicken embryos at E (embryonic)10, E14, and E18. Results: In total, 1,600, 4,610, and 2,166 DE (differentially expressed) mRNAs, 210, 573, and 234 DE lncRNAs (long non-coding RNAs), and 52, 137, and 33 DE miRNAs (microRNAs) were detected between E10 and E14, E10 and E18, and E14 and E18, respectively. Functional prediction showed several DE mRNAs and the target mRNAs of DE lncRNAs and DE miRNAs were significantly enriched in sarcomere organization, actin cytoskeleton organization, myofibril, muscle fiber development, and other terms and pathways related to muscle growth and development. Finally, a lncRNA-miRNA-mRNA ceRNA (competing endogenous RNA) network associated with muscle growth and development, which contained 6 DE lncRNAs, 13 DE miRNAs, and 50 DE mRNAs, was constructed based on the screened DE RNAs by Gene Ontology (GO) enrichment. These DE RNAs may play a critical regulatory role in the skeletal muscle development of chickens. Discussion: The results provide a genomic resource for mRNAs, lncRNAs, and miRNAs potentially involved in the skeletal muscle development of chickens, which lay the foundation for further studies of the molecular mechanisms underlying skeletal muscle growth and development in Tibetan chickens.
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Affiliation(s)
- Jie Li
- Laboratory of Ministry of Education for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, Sichuan, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan, China
| | - Chuwen Chen
- Laboratory of Ministry of Education for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, Sichuan, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan, China
| | - Ruipeng Zhao
- Laboratory of Ministry of Education for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, Sichuan, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan, China
| | - Jinbo Wu
- Institute of Science and Technology of Aba Tibetan and Qiang Autonomous Prefecture, Aba Sichuan, China
| | - Zhixiong Li
- Laboratory of Ministry of Education for Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, Sichuan, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, Sichuan, China
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Yu Z, Xu X, Ai N, Wang K, Zhang P, Li X, LiuFu S, Liu X, Jiang J, Gu J, Gao N, Ma H. Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig. Front Cell Dev Biol 2023; 11:1185823. [PMID: 37465009 PMCID: PMC10350537 DOI: 10.3389/fcell.2023.1185823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and 210 days after birth, n = 3) by histological analysis and whole transcriptome sequencing. Additionally, the study investigated the expression patterns of various RNAs involved in muscle fiber transformation and constructed a regulatory network for competing endogenous RNA (ceRNA) that includes circular RNA (circRNA)/long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA). Results: Histomorphology analysis showed that the diameter of muscle fiber reached its maximum at 150 days after birth. The slow muscle fiber transformation showed a pattern of initial decrease followed by an increase. 29,963 circRNAs, 2,683 lncRNAs, 986 miRNAs and 22,411 mRNAs with expression level ≥0 were identified by whole transcriptome sequencing. Furthermore, 642 differentially expressed circRNAs (DEc), 505 differentially expressed lncRNAs (DEl), 316 differentially expressed miRNAs (DEmi) and 6,090 differentially expressed mRNAs (DEm) were identified by differential expression analysis. Functions of differentially expressed mRNA were identified by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). GO enrichment analysis indicates that 40 known genes and 6 new genes are associated with skeletal muscle development. Additionally, KEGG analysis shows that these genes regulate skeletal muscle development via MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF and other signaling pathways. Through protein-protein interaction (PPI) and transcription factor prediction (TFP), the action mode of skeletal muscle-related genes was explored. PPI analysis showed that there were stable interactions among 19 proteins, meanwhile, TFP analysis predicted 22 transcription factors such as HMG20B, MYF6, MYOD1 and MYOG, and 12 of the 19 interacting proteins were transcription factors. The regulatory network of ceRNA related to skeletal muscle development was constructed based on the correlation of various RNA expression levels and the targeted binding characteristics with miRNA. The regulatory network included 31 DEms, 59 miRNAs, 667 circRNAs and 224 lncRNAs. conclusion: Overall, the study revealed the role of ceRNA regulatory network in the transformation of skeletal muscle fiber types in Ningxiang pigs, which contributes to the understanding of ceRNA regulatory network in Ningxiang pigs during the skeletal muscle development period.
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Affiliation(s)
- Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Kaiming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwen Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Sui LiuFu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Sawano S, Fukushima M, Akasaka T, Nakamura M, Tatsumi R, Ikeuchi Y, Mizunoya W. Up- and Downregulated Genes after Long-Term Muscle Atrophy Induced by Denervation in Mice Detected Using RNA-Seq. Life (Basel) 2023; 13:life13051111. [PMID: 37240756 DOI: 10.3390/life13051111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Skeletal muscle atrophy occurs rapidly as a result of inactivity. Although there are many reports on changes in gene expression during the early phase of muscle atrophy, the patterns of up-and downregulated gene expression after long-term and equilibrated muscle atrophy are poorly understood. In this study, we comprehensively examined the changes in gene expression in long-term denervated mouse muscles using RNA-Seq. The murine right sciatic nerve was denervated, and the mice were housed for five weeks. The cross-sectional areas of the hind limb muscles were measured using an X-ray CT system 35 days after denervation. After 28 d of denervation, the cross-sectional area of the muscle decreased to approximately 65% of that of the intact left muscle and reached a plateau. Gene expression in the soleus and extensor digitorum longus (EDL) muscles on the 36th day was analyzed using RNA-Seq and validated using RT-qPCR. RNA-Seq analysis revealed that three genes-Adora1, E230016M11Rik, and Gm10718-were upregulated and one gene-Gm20515-was downregulated in the soleus muscle; additionally, four genes-Adora1, E230016M11Rik, Pigh, and Gm15557-were upregulated and one gene-Fzd7-was downregulated in the EDL muscle (FDR < 0.05). Among these genes, E230016M11Rik, one of the long non-coding RNAs, was significantly upregulated in both the muscles. These findings indicate that E230016M11Rik could be a candidate gene for the maintenance of atrophied skeletal muscle size and an atrophic state.
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Affiliation(s)
- Shoko Sawano
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Department of Food and Life Science, School of Life and Environmental Science, Azabu University, Sagamihara 252-5201, Japan
| | - Misaki Fukushima
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Taiki Akasaka
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Mako Nakamura
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Ryuichi Tatsumi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yoshihide Ikeuchi
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Wataru Mizunoya
- Department of Animal and Marine Bioresource Sciences, Graduate School of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara 252-5201, Japan
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Li M, Liu Q, Xie S, Fu C, Li J, Tian C, Li X, Li C. LncRNA TCONS_00323213 Promotes Myogenic Differentiation by Interacting with PKNOX2 to Upregulate MyoG in Porcine Satellite Cells. Int J Mol Sci 2023; 24:ijms24076773. [PMID: 37047747 PMCID: PMC10094759 DOI: 10.3390/ijms24076773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Myogenic differentiation is a complex biological process that is regulated by multiple factors, among which long noncoding RNAs (lncRNAs) play an essential role. However, in-depth studies on the regulatory mechanisms of long noncoding RNAs (lncRNAs) in myogenic differentiation are limited. In this study, we characterized the role of the novel lncRNA TCONS_00323213, which is upregulated during porcine skeletal muscle satellite cell (PSC) differentiation in myogenesis. We found that TCONS_00323213 affected the proliferation and differentiation of PSC in vitro. We performed quantitative polymerase chain reaction (qPCR), 5-ethynyl-20-deoxyuridine (EdU), western blotting, immunofluorescence staining, pull-down assays, and cleavage under targets and tagmentation (CUT and Tag) assays to clarify the effects and action mechanisms of TCONS_00323213. LncRNA TCONS_00323213 inhibited myoblast proliferation based on analyses of cell survival rates during PSC proliferation. Functional analyses revealed that TCONS_00323213 promotes cell differentiation and enhances myogenin (MyoG), myosin heavy chain (MyHC), and myocyte enhancer factor 2 (MEF2C) during myoblast differentiation. As determined by pull-down and RNA immunoprecipitation (RIP) assays, the lncRNA TCONS_00323213 interacted with PBX/Knotted Homeobox 2 (PKNOX2). CUT and Tag assays showed that PKNOX2 was significantly enriched on the MyoG promoter after lncRNA TCONS_00323213 knockdown. Our findings demonstrate that the interaction between lncRNA TCONS_00323213 and PKNOX2 relieves the inhibitory effect of PKNOX2 on the MyoG promoter, increases its expression, and promotes PSC differentiation. This novel role of lncRNA TCONS_00323213 sheds light on the molecular mechanisms by which lncRNAs regulate porcine myogenesis.
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Affiliation(s)
- Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Quan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Su Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Chong Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Tian
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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Yang C, Zhou X, Xue Y, Li D, Wang L, Zhong T, Dai D, Cao J, Guo J, Li L, Zhang H, Zhan S. Transcriptome Analysis Reveals the Profile of Long Non-Coding RNAs during Myogenic Differentiation in Goats. Int J Mol Sci 2023; 24:ijms24076370. [PMID: 37047345 PMCID: PMC10094361 DOI: 10.3390/ijms24076370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) are emerging as essential regulators of the growth and development of skeletal muscles. However, little is known about the expression profiles of lncRNAs during the proliferation and differentiation of skeletal muscle satellite cells (MuSCs) in goats. In this study, we investigate potential regulatory lncRNAs that govern muscle development by performing lncRNA expression profiling analysis during the proliferation (cultured in the growth medium, GM) and differentiation (cultured in the differentiation medium, DM1/DM5) of MuSCs. In total, 1001 lncRNAs were identified in MuSC samples, and 314 differentially expressed (DE) (FDR < 0.05, |log2FC| > 1) lncRNAs were screened by pairwise comparisons from three comparison groups (GM-vs-DM1, GM-vs-DM5, DM1-vs-DM5). Moreover, we identified the cis-, trans-, and antisense-regulatory target genes of DE lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these target genes were significantly enriched in muscle development-related GO terms and KEGG pathways. In addition, the network of interactions between DE lncRNAs and their target genes was identified, which included well-known myogenesis regulators such as Myogenic differentiation 1 (MyoD), Myogenin (MyoG), and Myosin heavy chain (MyHC). Meanwhile, competing endogenous RNA (ceRNA) network analysis showed that 237 DE lncRNAs could bind to 329 microRNAs (miRNAs), while miRNAs could target 564 mRNAs. Together, our results provide a genome-wide resource of lncRNAs that may contribute to myogenic differentiation in goats and lay the groundwork for future investigation into their functions during skeletal muscle development.
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