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Ma M, Chen M, Wu X, Sooranna SR, Liu Q, Shi D, Wang J, Li H. A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells. Epigenetics 2023; 18:2270864. [PMID: 37910666 PMCID: PMC10768731 DOI: 10.1080/15592294.2023.2270864] [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: 12/05/2022] [Accepted: 09/01/2023] [Indexed: 11/03/2023] Open
Abstract
Cattle skeletal muscle development is a complex and highly coordinated biological process mediated by a series of myogenic regulators, which plays a critical role in beef yield and quality. Long non-coding RNAs (lncRNAs) have been shown to regulate skeletal muscle development. However, the molecular mechanism by which lncRNAs regulate skeletal muscle development is largely unknown. We performed transcriptome analysis of muscle tissues of adult and embryo Angus cattle to investigate the mechanism by which lncRNA regulates skeletal muscle development between adult and embryo cattle. A total of 37,115 candidate lncRNAs were detected, and a total of 1,998 lncRNAs were differentially expressed between the muscle tissue libraries of adult and embryo cattle, including 1,229 up-regulated lncRNAs and 769 down-regulated lncRNAs (adult cattle were the control group). We verified the expression of 7 differentially expressed lncRNAs by quantitative real-time PCR (RT-qPCR), and analysed the tissue expression profile of lnc000100, which is down-regulated in the longest dorsal muscle during foetal life and which is highly specifically expressed in muscle tissue. We found that the interference of lnc000100 significantly inhibited cell proliferation and promoted cell differentiation. Lnc000100 was located in the nucleus by RNA-FISH. Our research provides certain resources for the analysis of lncRNA regulating cattle skeletal muscle development, and may also provide new insights for improving beef production and breed selection.
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Affiliation(s)
- Mengke Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Suren R. Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Jian Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
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Ma Y, Zhao T, Wu X, Yang Z, Sun Y. Expression profile and functional prediction of novel LncRNA 5.8S rRNA-OT1 in cattle. Anim Biotechnol 2023; 34:2040-2050. [PMID: 35465841 DOI: 10.1080/10495398.2022.2066540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Long non-coding RNAs (LncRNAs) are generally longer than 200 bp in length and play an important regulatory role in the growth and development of skeletal muscle. In the previous work, the non-coding RNAs with abundant expression in bovine tissues were screened out. After quantitative real-time PCR (qPCR), 33 lncRNAs with differential expression in various bovine tissues were identified. Differential expression analysis base on tissue expression profiles of 33 lncRNAs, a long non-coding RNA LncRNA13, which may have effects on bovine muscle development, was found. The expression levels in embryo muscle and adult cattle muscle were significantly different (p < 0.01), so it is speculated that it may have a certain impact on the development of cattle muscle. It was named LncRNA 5.8S rRNA-OT1, and its overexpression vector pcDNA3.1-LncRNA 5.8S rRNA-OT1 was cloned and constructed. The purpose of this study is to further explore its impact on the proliferation and differentiation of bovine muscle cells and accumulate data to lay a foundation for further exploration of the function of LncRNA 5.8S rRNA-OT1 and add basic data for the study of the regulatory mechanism of lncRNA.
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Affiliation(s)
- Yaoyao Ma
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tianqi Zhao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinyi Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Yang Y, Wu J, Liu W, Zhao Y, Chen H. The Function and Regulation Mechanism of Non-Coding RNAs in Muscle Development. Int J Mol Sci 2023; 24:14534. [PMID: 37833983 PMCID: PMC10572267 DOI: 10.3390/ijms241914534] [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: 06/09/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023] Open
Abstract
Animal skeletal muscle growth is regulated by a complex molecular network including some non-coding RNAs (ncRNAs). In this paper, we review the non-coding RNAs related to the growth and development of common animal skeletal muscles, aiming to provide a reference for the in-depth study of the role of ncRNAs in the development of animal skeletal muscles, and to provide new ideas for the improvement of animal production performance.
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Affiliation(s)
- Yaling Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| | - Jian Wu
- Key Laboratory of Beef Cattle Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Academy of Agricultural Sciences of Jilin Province, Changchun 136100, China;
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| | - Yumin Zhao
- Key Laboratory of Beef Cattle Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Academy of Agricultural Sciences of Jilin Province, Changchun 136100, China;
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
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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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Liu S, Tao X, Deng B, Li Y, Xu Z. Genome-Wide Analysis of Long Noncoding RNAs in Porcine Intestine during Weaning Stress. Int J Mol Sci 2023; 24:5343. [PMID: 36982414 PMCID: PMC10049174 DOI: 10.3390/ijms24065343] [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: 01/12/2023] [Revised: 02/18/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in various biological processes, and they are considered to be closely associated with the pathogenesis of intestinal diseases. However, the role and expression of lncRNAs in intestinal damage during weaning stress remain unknown. Herein, we investigated the expression profiles of jejunal tissue from weaning piglets at 4 and 7 d after weaning (groups W4 and W7, respectively) and from suckling piglets on the same days (groups S4 and S7, respectively). Genome-wide analysis of lncRNAs was also performed using RNA sequencing technology. A total of 1809 annotated lncRNAs and 1612 novel lncRNAs were obtained from the jejunum of piglets. In W4 vs. S4, a total of 331 lncRNAs showed significant differential expression, and a total of 163 significantly differentially expressed lncRNAs (DElncRNAs) was identified in W7 vs. S7. Biological analysis indicated that DElncRNAs were involved in intestinal diseases, inflammation, and immune functions, and were mainly enriched in the Jak-STAT signaling pathway, inflammatory bowel disease, T cell receptor signaling pathway, B cell receptor signaling pathway and intestinal immune network for IgA production. Moreover, we found that lnc_000884 and target gene KLF5 were significantly upregulated in the intestine of weaning piglets. The overexpression of lnc_000884 also significantly promoted the proliferation and depressed apoptosis of IPEC-J2 cells. This result suggested that lnc_000884 may contribute to repairing intestinal damage. Our study identified the characterization and expression profile of lncRNAs in the small intestine of weaning piglets and provided new insights into the molecular regulation of intestinal damage during weaning stress.
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Affiliation(s)
| | | | | | | | - Ziwei Xu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, 298 Desheng Middle Road, Hangzhou 310021, China
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Wei Y, Qi T, Cao S, Zhang W, Yu F, Zeng H, Weng J. LncRNA XLOC_015548 affects the proliferation and differentiation of myoblasts via the MAPK signaling pathway. Exp Biol Med (Maywood) 2023; 248:469-480. [PMID: 36852460 PMCID: PMC10281533 DOI: 10.1177/15353702231151963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/11/2022] [Indexed: 03/01/2023] Open
Abstract
In recent years, an increasing number of studies have reported that long non-coding RNAs (lncRNAs) play essential regulatory roles in myogenic differentiation. In this study, a specific LncRNA XLOC_015548 (Lnc000280) was identified. However, little research has explored its mechanism of action by constructing XLOC_015548 gene editing cell models. In this study, relevant sequences were obtained according to the RNA-seq results. Subsequently, XLOC_015548 knockdown and over-expression lentiviral vectors were constructed, and the C2C12 myoblast cell line was transfected to prepare the XLOC_015548 gene-edited myoblast model. The in vitro analysis revealed that over-expression of XLOC_015548 significantly promoted the proliferation and differentiation of myoblasts and the formation of myotubes, whereas the opposite result was obtained in the knockdown group. XLOC_015548 regulated myogenic differentiation and affected the expression of myogenic differentiation regulators such as Myod, myogenin, and MyHC. Regarding the signaling pathway, we found that XLOC_015548 correlated with the phosphorylation level of MAPK/MEK/ERK pathway proteins. And the degree of phosphorylation was positively correlated with the protein expression of myogenic differentiation regulators. In conclusion, a new gene-edited myoblast model was constructed based on the lncRNA regulator XLOC_015548. The in vitro cell experiments verified that XLOC_015548 had regulatory effects on muscle growth and myoblast differentiation. These findings provide a laboratory foundation for the clinical application of lncRNAs as regulatory factors in the treatment of disuse muscle atrophy.
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Affiliation(s)
- Yihao Wei
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Shantou University Medical College, Shantou 515000, China
| | - Tiantian Qi
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Siyang Cao
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Weifei Zhang
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Fei Yu
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Hui Zeng
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jian Weng
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen 518036, China
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He Z, Wang X, Qi Y, Zhu C, Zhao Z, Zhang X, Liu X, Li S, Zhao F, Wang J, Shi B, Hu J. Long-stranded non-coding RNAs temporal-specific expression profiles reveal longissimus dorsi muscle development and intramuscular fat deposition in Tianzhu white yak. J Anim Sci 2023; 101:skad394. [PMID: 38029315 PMCID: PMC10760506 DOI: 10.1093/jas/skad394] [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: 07/02/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023] Open
Abstract
The process of muscle development and intramuscular fat (IMF) deposition is quite complex and controlled by both mRNAs and ncRNAs. Long-stranded non-coding RNAs (LncRNAs) are involved in various biological processes in mammals while also playing a critical role in muscle development and fat deposition. In the present study, RNA-Seq was used to comprehensively study the expression of lncRNAs and mRNAs during muscle development and intramuscular fat deposition in postnatal Tianzhu white yaks at three stages, including 6 mo of age (calve, n = 6), 30 mo of age (young cattle, n = 6) and 54 mo of age (adult cattle, n = 6). The results indicated that a total of 2,101 lncRNAs and 20,855 mRNAs were screened across the three stages, of which the numbers of differential expression (DE) lncRNAs and DE mRNAs were 289 and 1,339, respectively, and DE lncRNAs were divided into eight different expression patterns based on expression trends. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that some DE mRNAs overlapped with target genes of lncRNAs, such as NEDD4L, SCN3B, AGT, HDAC4, DES, MYH14, KLF15 (muscle development), ACACB, PCK2, LIPE, PIK3R1, PNPLA2, and MGLL (intramuscular fat deposition). These DE mRNAs were significantly enriched in critical muscle development and IMF deposition-related pathways and GO terms, such as AMPK signaling pathway, PI3K-Akt signaling pathway, PPAR signaling pathway, etc. In addition, lncRNA-mRNA co-expression network analysis revealed that six lncRNAs (MSTRG.20152.2, MSTRG.20152.3, XR_001351700.1, MSTRG.8190.1, MSTRG.4827.1, and MSTRG.11486.1) may play a major role in Tianzhu white yak muscle development and lipidosis deposition. Therefore, this study enriches the database of yak lncRNAs and could help to further explore the functions and roles of lncRNAs in different stages of muscle development and intramuscular fat deposition in the Tianzhu white yak.
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Affiliation(s)
- Zhaohua He
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiangyan Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Youpeng Qi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Chune Zhu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolan Zhang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Zhang J, Sheng H, Pan C, Wang S, Yang M, Hu C, Wei D, Wang Y, Ma Y. Identification of key genes in bovine muscle development by co-expression analysis. PeerJ 2023; 11:e15093. [PMID: 37070092 PMCID: PMC10105563 DOI: 10.7717/peerj.15093] [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: 11/25/2022] [Accepted: 02/27/2023] [Indexed: 04/19/2023] Open
Abstract
Background Skeletal muscle is not only an important tissue involved in exercise and metabolism, but also an important part of livestock and poultry meat products. Its growth and development determines the output and quality of meat to a certain extent, and has an important impact on the economic benefits of animal husbandry. Skeletal muscle development is a complex regulatory network process, and its molecular mechanism needs to be further studied. Method We used a weighted co-expression network (WGCNA) and single gene set enrichment analysis (GSEA) to study the RNA-seq data set of bovine tissue differential expression analysis, and the core genes and functional enrichment pathways closely related to muscle tissue development were screened. Finally, the accuracy of the analysis results was verified by tissue expression profile detection and bovine skeletal muscle satellite cell differentiation model in vitro (BSMSCs). Results In this study, Atp2a1, Tmod4, Lmod3, Ryr1 and Mybpc2 were identified as marker genes in muscle tissue, which are mainly involved in glycolysis/gluconeogenesis, AMPK pathway and insulin pathway. The assay results showed that these five genes were highly expressed in muscle tissue and positively correlated with the differentiation of bovine BSMSCs. Conclusions In this study, several muscle tissue characteristic genes were excavated, which may play an important role in muscle development and provide new insights for bovine molecular genetic breeding.
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Affiliation(s)
| | | | | | | | | | | | | | - Yachun Wang
- China Agricultural University, Beijing, China
| | - Yun Ma
- Ningxia University, Yinchuan, China
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Lee DY, Lee SY, Jung JW, Kim JH, Oh DH, Kim HW, Kang JH, Choi JS, Kim GD, Joo ST, Hur SJ. Review of technology and materials for the development of cultured meat. Crit Rev Food Sci Nutr 2022; 63:8591-8615. [PMID: 35466822 DOI: 10.1080/10408398.2022.2063249] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cultured meat production technology suggested that can solve the problems of traditional meat production such as inadequate breeding environment, wastewater, methane gas generation, and animal ethics issues. Complementing cultured meat production methods, sales and safety concerns will make the use of cultured meat technology easier. This review contextualizes the commercialization status of cultured meat and the latest technologies and challenges associated with its production. Investigation was conducted on materials and basic cell culture technique for cultured meat culture is presented. The development of optimal cultured meat technology through these studies will be an innovative leap in food technology. The process of obtaining cells from animal muscle, culturing cells, and growing cells into meat are the basic processes of cultured meat production. The substances needed to production of cultured meat were antibiotics, digestive enzymes, basal media, serum or growth factors. Although muscle cells have been produced closer to meat due to the application of scaffolds materials and 3 D printing technology, still a limit to reducing production costs enough to be used as foods. In addition, developing edible materials is also a challenge because the materials used to produce cultured meat are still not suitable for food sources.
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Affiliation(s)
- Da Young Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Seung Yun Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Jae Won Jung
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Jae Hyun Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Dong Hun Oh
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Hyun Woo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Ji Hyeop Kang
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
| | - Jung Seok Choi
- Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Gap-Don Kim
- Graduate School of International Agricultural Technology, Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, Kangwong, Korea
| | - Seon-Tea Joo
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Gyeongnam, Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi, Korea
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Bao G, Li S, Zhao F, Wang J, Liu X, Hu J, Shi B, Wen Y, Zhao L, Luo Y. Comprehensive Transcriptome Analysis Reveals the Role of lncRNA in Fatty Acid Metabolism in the Longissimus Thoracis Muscle of Tibetan Sheep at Different Ages. Front Nutr 2022; 9:847077. [PMID: 35369085 PMCID: PMC8964427 DOI: 10.3389/fnut.2022.847077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/11/2022] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNA (lncRNA) plays an important regulatory role in mammalian adipogenesis and lipid metabolism. However, their function in the longissimus thoracis (LT) muscle of fatty acid metabolism of Tibetan sheep remains undefined. In this study, fatty acid and fat content in LT muscle of Tibetan sheep were determined, and RNA sequencing was performed to reveal the temporal regularity of lncRNA expression and the effect of lncRNA-miRNA-mRNA ceRNA regulatory network on lipid metabolism of LT muscle in Tibetan sheep at four growth stages (4-month-old, 4 m; 1.5-year-old, 1.5 y; 3.5-year-old, 3.5 y; 6-year-old, 6 y). The results indicated that the intramuscular fat (IMF) content was highest at 1.5 y. Moreover, the monounsaturated fatty acid (MUFA) content in 1.5 y of Tibetan sheep is significantly higher than those of the other groups (P < 0.05), and it was also rich in a variety of polyunsaturated fatty acids (PUFA). A total of 360 differentially expressed lncRNAs (DE lncRNAs) were identified from contiguous period transcriptome comparative groups of 4 m vs. 1.5 y, 1.5 y vs. 3.5 y, 3.5 y vs. 6 y, and 4 m vs. 6 y, respectively. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis found that the target genes in lncRNA trans-mRNA were significantly related to the protein digestion, absorption, and fatty acid biosynthesis pathways (P < 0.05), which demonstrated that DE lncRNA trans-regulated the target genes, and further regulated the growth and development of the LT muscle and intramuscular fatty acid metabolism in Tibetan sheep. We further analyzed the role of the lncRNA-miRNA-mRNA regulatory network in the lipid metabolism of Tibetan sheep. Additionally, GPD2, LIPE (lipase E hormone-sensitive enzyme), TFDP2, CPT1A, ACACB, ADIPOQ, and other mRNA related to fatty acid and lipid metabolism and the corresponding lncRNA-miRNA regulatory pairs were identified. The enrichment analysis of mRNA in the regulatory network found that the AMPK signaling pathway was the most significantly enriched (P = 0.0000112361). Comprehensive transcriptome analysis found that the LIPE, ADIPOQ, ACACB, and CPT1A that were regulated by lncRNA might change the formation of energy metabolism in Tibetan sheep muscle through the AMPK signaling pathway, and oxidized muscle fibers are transformed into glycolytic muscle fibers, reduced IMF content, and the fatty acid profile also changed.
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Affiliation(s)
- Gaoliang Bao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuliang Wen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Li Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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11
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Muniz MMM, Simielli Fonseca LF, Scalez DCB, Vega AS, dos Santos Silva DB, Ferro JA, Chardulo AL, Baldi F, Cánovas A, de Albuquerque LG. Characterization of novel
lncRNA
muscle expression profiles associated with meat quality in beef cattle. Evol Appl 2022; 15:706-718. [PMID: 35505883 PMCID: PMC9046762 DOI: 10.1111/eva.13365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to identify novel lncRNA differentially expressed (DE) between divergent animals for beef tenderness and marbling traits in Nellore cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (of 80 bulls set) for tenderness, tender (n = 10) and tough (n = 10) groups, and marbling trait, high (n = 10) and low (n = 10) groups were used to perform transcriptomic analysis using RNA‐Sequencing. For tenderness, 29 lncRNA were DE (p‐value ≤ 0.01) in tough beef animals in relation to tender beef animals. We observed that genic lncRNAs, for example, lncRNA_595.1, were overlapping exonic part of the PICK gene, while lncRNA_3097.2 and lncRNA_3129.5 overlapped intronic part of the genes GADL1 and PSMD6. The lncRNA associated with PICK1, GADL1, and PMD6 genes were enriched in the pathways associated with the ionotropic glutamate receptor, gamma‐aminobutyric acid synthesis, and the ubiquitin–proteasome pathway. For marbling, 50 lncRNA were DE (p‐value ≤ 0.01) in high marbling group compared with low marbling animals. The genic lncRNAs, such as lncRNA_3191.1, were overlapped exonic part of the ITGAL gene, and the lncRNA_512.1, lncRNA_3721.1, and lncRNA_41.4 overlapped intronic parts of the KRAS and MASP1 genes. The KRAS and ITGAL genes were enriched in pathways associated with integrin signaling, which is involved in intracellular signals in response to the extracellular matrix, including cell form, mobility, and mediates progression through the cell cycle. In addition, the lincRNAs identified to marbling trait were associated with several genes related to calcium binding, muscle hypertrophy, skeletal muscle, lipase, and oxidative stress response pathways that seem to play a role important in the physiological processes related to meat quality. These findings bring new insights to better understand the biology mechanisms involved in the gene regulation of these traits, which will be valuable for a further investigation of the interactions between lncRNA and mRNAs, and of how these interactions may affect meat quality traits.
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Affiliation(s)
- Maria Malane Magalhães Muniz
- São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal SP Brazil
- Centre for Genetic Improvement of Livestock Department of Animal Biosciences University of Guelph Guelph Canada
| | | | | | - Aroa Suarez Vega
- Centre for Genetic Improvement of Livestock Department of Animal Biosciences University of Guelph Guelph Canada
| | | | - Jesus Aparecido Ferro
- São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal SP Brazil
- National Council for Scientific and Technological Development (CNPq) Brazil
| | - Artur Loyola Chardulo
- São Paulo State University (Unesp) College of Veterinary and Animal Science Botucatu SP Brazil
- National Council for Scientific and Technological Development (CNPq) Brazil
| | - Fernando Baldi
- São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal SP Brazil
- National Council for Scientific and Technological Development (CNPq) Brazil
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock Department of Animal Biosciences University of Guelph Guelph Canada
| | - Lucia Galvão de Albuquerque
- São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal SP Brazil
- National Council for Scientific and Technological Development (CNPq) Brazil
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12
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Liu C, Liu L, Gao J, Wang J, Liu Y. Identification of Two Long Non-Coding RNAs AC010082.1 and AC011443.1 as Biomarkers of Coronary Heart Disease Based on Logistic Stepwise Regression Prediction Model. Front Genet 2021; 12:780431. [PMID: 34868268 PMCID: PMC8637336 DOI: 10.3389/fgene.2021.780431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Coronary heart disease (CHD) is a global health concern with high morbidity and mortality rates. This study aimed to identify the possible long non-coding RNA (lncRNA) biomarkers of CHD. The lncRNA- and mRNA-related data of patients with CHD were downloaded from the Gene Expression Omnibus database (GSE113079). The limma package was used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs, respectively). Then, miRcode, TargetScan, miRDB, and miRTarBase databases were used to form the competing endogenous RNA (ceRNA) network. Furthermore, SPSS Modeler 18.0 was used to construct a logistic stepwise regression prediction model for CHD diagnosis based on DElncRNAs. Of the microarray data, 70% was used as a training set and 30% as a test set. Moreover, a validation cohort including 30 patients with CHD and 30 healthy controls was used to verify the hub lncRNA expression through real-time reverse transcription-quantitative PCR (RT-qPCR). A total of 185 DElncRNAs (114 upregulated and 71 downregulated) and 382 DEmRNAs (162 upregulated and 220 downregulated) between CHD and healthy controls were identified from the microarray data. Furthermore, through bioinformatics prediction, a 38 lncRNA-21miRNA-40 mRNA ceRNA network was constructed. Next, by constructing a logistic stepwise regression prediction model for 38 DElncRNAs, we screened two hub lncRNAs AC010082.1 and AC011443.1 (p < 0.05). The sensitivity, specificity, and area under the curve were 98.41%, 100%, and 0.995, respectively, for the training set and 93.33%, 91.67%, and 0.983, respectively, for the test set. We further verified the significant upregulation of AC010082.1 (p < 0.01) and AC011443.1 (p < 0.05) in patients with CHD using RT-qPCR in the validation cohort. Our results suggest that lncRNA AC010082.1 and AC011443.1 are potential biomarkers of CHD. Their pathological mechanism in CHD requires further validation.
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Affiliation(s)
- Chao Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Lanchun Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Jialiang Gao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Key Technology Laboratory of Cardiovascular Disease-Syndrome Combination, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongmei Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.,Key Technology Laboratory of Cardiovascular Disease-Syndrome Combination, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
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13
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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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14
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An Emerging Role for Epigenetics in Cerebral Palsy. J Pers Med 2021; 11:jpm11111187. [PMID: 34834539 PMCID: PMC8625874 DOI: 10.3390/jpm11111187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 12/29/2022] Open
Abstract
Cerebral palsy is a set of common, severe, motor disabilities categorized by a static, nondegenerative encephalopathy arising in the developing brain and associated with deficits in movement, posture, and activity. Spastic CP, which is the most common type, involves high muscle tone and is associated with altered muscle function including poor muscle growth and contracture, increased extracellular matrix deposition, microanatomic disruption, musculoskeletal deformities, weakness, and difficult movement control. These muscle-related manifestations of CP are major causes of progressive debilitation and frequently require intensive surgical and therapeutic intervention to control. Current clinical approaches involve sophisticated consideration of biomechanics, radiologic assessments, and movement analyses, but outcomes remain difficult to predict. There is a need for more precise and personalized approaches involving omics technologies, data science, and advanced analytics. An improved understanding of muscle involvement in spastic CP is needed. Unfortunately, the fundamental mechanisms and molecular pathways contributing to altered muscle function in spastic CP are only partially understood. In this review, we outline evidence supporting the emerging hypothesis that epigenetic phenomena play significant roles in musculoskeletal manifestations of CP.
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15
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Yao Z, Yuan Z, Bai Y, Gu H, Jia H, Liu D, Yang Z, Wang W. Altered mRNA and lncRNA expression profiles in the striated muscle complex of anorectal malformation rats. Pediatr Surg Int 2020; 36:1287-1297. [PMID: 32915273 DOI: 10.1007/s00383-020-04741-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Striated muscle complex (SMC) dysplasia has been confirmed to contribute to postoperative defecation dysfunction of patients with anorectal malformations (ARMs). To date, the potential molecular mechanisms of SMC dysplasia underlying the development of ARMs have not been clearly explained. This study examined the expression profiles of mRNAs and lncRNAs in the malformed SMC of ARM rats using RNA sequencing (RNA-seq). METHODS A rat model of ARMs was established by the intragastric administration of 1% ethylene thiourea (ETU) on an embryonic day 10 (E10). The rats were subjected to euthanasia and the SMC samples were collected on E19. The expression of mRNAs and lncRNAs was analyzed by RNA-seq on the Illumina HiSeq2500 platform. qRT-PCR was used to confirm the results of RNA-seq. RESULTS Compared with the levels in control rats, 1408 mRNAs and 472 lncRNAs were differentially expressed in the SMC of E19 ARM rats. GO and KEGG pathway analyses showed that the top enriched GO terms were mainly related to muscle development and the enriched pathways were associated with muscle and synaptic development. Protein-protein interaction network analysis was also performed using the STRING database. The network map revealed the interaction between the WNT3 protein and NTRK1, NTF4, MUSK, and BMP5 proteins. Finally, the qRT-PCR results further confirmed the RNA-seq data. CONCLUSION Our findings indicate the involvement of these dysregulated mRNAs and lncRNAs in the pathogenesis of SMC dysplasia in ARMs, providing a theoretical foundation for developing interventions to improve postoperative defecation function.
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Affiliation(s)
- Zhiya Yao
- Department of Pediatric Surgery, Shengjing Hospital, China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital, China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, People's Republic of China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital, China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, People's Republic of China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, Liaoning, 110004, People's Republic of China
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital, China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, People's Republic of China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital, China Medical University, 36 Sanhao Street, Shenyang, Liaoning, 110004, People's Republic of China.
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16
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Chen W, Lv X, Wang Y, Zhang X, Wang S, Hussain Z, Chen L, Su R, Sun W. Transcriptional Profiles of Long Non-coding RNA and mRNA in Sheep Mammary Gland During Lactation Period. Front Genet 2020; 11:946. [PMID: 33101361 PMCID: PMC7546800 DOI: 10.3389/fgene.2020.00946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
Sheep milk and related products have been growing in popularity around the world in recent years. However, the sheep milk industry is limited by low milk yield, and the molecular regulators of ovine lactation remain largely unknown. To investigate the transcriptomic basis of sheep lactation, RNA-Sequencing was used to explore the expression profiles of lncRNA and mRNA of the mammary gland in Hu sheep at three key time points during the lactation stage: 5 days before the expected date of parturition perinatal period (PP), 6 days after parturition early lactation (EL), and 25 days after parturition peak lactation (PL). A total of 1111, 688, and 54 differentially expressed (DE) lncRNAs as well as 1360, 660, and 17 DE mRNAs were detected in the EL vs PP, PL vs PP, and PL vs EL comparisons, respectively. Several prominent mRNAs (e.g., CSN1S1, CSN1S2, PAEP, CSN2, CSN3, and COL3A1) and lncRNAs (e.g., LNC_018483, LNC_005678, LNC_012936, and LNC_004856) were identified. Functional enrichment analysis revealed that several DE mRNAs and target genes of DE lncRNAs were involved in lactation-related pathways, such as MAPK, PPAR, and ECM-receptor interaction. This study enhances our understanding of how transcriptomic profiles change during the lactation period and pave the way for future studies examining sheep lactation.
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Affiliation(s)
- Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yue Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinjun Zhang
- Animal Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zahid Hussain
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ling Chen
- Animal Science and Veterinary Medicine Bureau of Suzhou City, Suzhou, China
| | - Rui Su
- Suzhou Taihu Dongshang Sheep Industry Development Co., Ltd., Suzhou, China
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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