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Feng X, Tong L, Ma L, Mu T, Yu B, Ma R, Li J, Wang C, Zhang J, Gu Y. Mining key circRNA-associated-ceRNA networks for milk fat metabolism in cows with varying milk fat percentages. BMC Genomics 2024; 25:323. [PMID: 38561663 PMCID: PMC10983688 DOI: 10.1186/s12864-024-10252-y] [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: 08/31/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Cow milk fat is an essential indicator for evaluating and measuring milk quality and cow performance. Growing research has identified the molecular functions of circular RNAs (circRNAs) necessary for mammary gland development and lactation in mammals. METHOD The present study analyzed circRNA expression profiling data in mammary epithelial cells (MECs) from cows with highly variable milk fat percentage (MFP) using differential expression analysis and weighted gene co-expression network analysis (WGCNA). RESULTS A total of 309 differentially expressed circRNAs (DE-circRNAs) were identified in the high and low MFP groups. WGCNA analysis revealed that the pink module was significantly associated with MFP (r = - 0.85, P = 0.007). Parental genes of circRNAs in this module were enriched mainly in lipid metabolism-related signaling pathways, such as focal adhesion, ECM-receptor interaction, adherens junction and AMPK. Finally, six DE-circRNAs were screened from the pink module: circ_0010571, circ_0007797, circ_0002746, circ_0003052, circ_0004319, and circ_0012840. Among them, circ_0002746, circ_0003052, circ_0004319, and circ_0012840 had circular structures and were highly expressed in mammary tissues. Subcellular localization revealed that these four DE-circRNAs may play a regulatory role in the mammary glands of dairy cows, mainly as competitive endogenous RNAs (ceRNAs). Seven hub target genes (GNB1, GNG2, PLCB1, PLCG1, ATP6V0C, NDUFS4, and PIGH) were obtained by constructing the regulatory network of their ceRNAs and then analyzed by CytoHubba and MCODE plugins in Cytoscape. Functional enrichment analysis revealed that these genes are crucial and most probable ceRNA regulators in milk fat metabolism. CONCLUSIONS Our study identified several vital circRNAs and ceRNAs affecting milk fat synthesis, providing new research ideas and a theoretical basis for cow lactation, milk quality, and breed improvement.
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Affiliation(s)
- Xiaofang Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Lijia Tong
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Lina Ma
- NingXia Academy of Agriculture and Forestry Sciences, 750002, Yinchuan, China
| | - Tong Mu
- School of Life Science, Yan'an University, 716000, Yanan, China
| | - Baojun Yu
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Ruoshuang Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Jiwei Li
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Chuanchuan Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China
| | - Juan Zhang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, China.
| | - Yaling Gu
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, 750021, Yinchuan, 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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3
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Zhao X, Ye J, Lin X, Xue H, Zou X, Liu G, Deng M, Sun B, Guo Y, Liu D, Li Y. Identification of Key Functional Genes and LncRNAs Influencing Muscle Growth and Development in Leizhou Black Goats. Genes (Basel) 2023; 14:genes14040881. [PMID: 37107639 PMCID: PMC10138011 DOI: 10.3390/genes14040881] [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: 03/01/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze differentially expressed genes. Expression levels of regulator of calcineurin 1 (RCAN1) and olfactory receptor 2AP1 (OR2AP1) were significantly different in LD muscles of goats aged 0, 3, and 6 months, indicating potentially important roles in postnatal muscle development. Differentially expressed lncRNAs and mRNAs were mainly enriched in biological processes and pathways related to cellular energy metabolism, consistent with previous studies. Three lncRNAs, TCONS_00074191, TCONS_00074190, and TCONS_00078361, may play a cis-acting role with methyltransferase-like 11B (METTL11B) genes and participate in the methylation of goat muscle proteins. Some of the identified genes may provide valuable resources for future studies on postnatal meat development in goat muscles.
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Affiliation(s)
- Xiuhui Zhao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Junning Ye
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Xunkai Lin
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Huiwen Xue
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
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4
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Shen J, Luo Y, Wang J, Hu J, Liu X, Li S, Hao Z, Li M, Zhao Z, Zhang Y, Yang S, Wang L, Gu Y. Integrated transcriptome analysis reveals roles of long non-coding RNAs (lncRNAs) in caprine skeletal muscle mass and meat quality. Funct Integr Genomics 2023; 23:63. [PMID: 36810929 DOI: 10.1007/s10142-023-00987-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/23/2023]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in the growth and development of skeletal muscle. However, there is limited information on goats. In this study, expression profiles of lncRNAs in Longissimus dorsi muscle from Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with divergent meat yield and meat quality were compared using RNA-sequencing. Based on our previous microRNA (miRNA) and mRNA profiles obtained from the same tissues, the target genes and binding miRNAs of differentially expressed lncRNAs were obtained. Subsequently, lncRNA-mRNA interaction networks and a ceRNA network of lncRNA-miRNA-mRNA were constructed. A total of 136 differentially expressed lncRNAs were identified between the two breeds. Fifteen cis target genes and 143 trans target genes were found for differentially expressed lncRNAs, and they were enriched in muscle contraction, muscle system process, muscle cell differentiation, and p53 signaling pathway. A total of 69 lncRNA-trans target gene pairs were constructed, with close relationship with muscle development, intramuscular fat deposition, and meat tenderness. A total of 16 lncRNA-miRNA-mRNA ceRNA pairs were identified, of which some reportedly associated with skeletal muscle development and fat deposition were found. The study will provide an improved understanding of the roles of lncRNAs in caprine meat yield and meat quality.
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Affiliation(s)
- Jiyuan Shen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuting Zhang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shutong Yang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Longbin Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuanhua Gu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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Lyu P, Jiang H. RNA-Sequencing Reveals Upregulation and a Beneficial Role of Autophagy in Myoblast Differentiation and Fusion. Cells 2022; 11:cells11223549. [PMID: 36428978 PMCID: PMC9688917 DOI: 10.3390/cells11223549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Myoblast differentiation is a complex process whereby the mononuclear muscle precursor cells myoblasts express skeletal-muscle-specific genes and fuse with each other to form multinucleated myotubes. The objective of this study was to identify potentially novel mechanisms that mediate myoblast differentiation. We first compared transcriptomes in C2C12 myoblasts before and 6 days after induction of myogenic differentiation by RNA-seq. This analysis identified 11,046 differentially expressed genes, of which 5615 and 5431 genes were upregulated and downregulated, respectively, from before differentiation to differentiation. Functional enrichment analyses revealed that the upregulated genes were associated with skeletal muscle contraction, autophagy, and sarcomeres while the downregulated genes were associated with ribonucleoprotein complex biogenesis, mRNA processing, ribosomes, and other biological processes or cellular components. Western blot analyses showed an increased conversion of LC3-I to LC3-II protein during myoblast differentiation, further demonstrating the upregulation of autophagy during myoblast differentiation. Blocking the autophagic flux in C2C12 cells with chloroquine inhibited the expression of skeletal-muscle-specific genes and the formation of myotubes, confirming a positive role for autophagy in myoblast differentiation and fusion.
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6
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Yao Y, Meng Z, Li W, Xu Y, Wang Y, Suolang S, Xi G, Cao L, Guo M. Profiling and Functional Analysis of long non-coding RNAs in yak healthy and atretic follicles. Anim Reprod 2022; 19:e20210131. [PMID: 36313598 PMCID: PMC9613354 DOI: 10.1590/1984-3143-ar2021-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
Yak is the livestock on which people live in plateau areas, but its fecundity is low. Follicular development plays a decisive role in yak reproductive performance. As an important regulatory factor, the expression of long non-coding RNA (lncRNAs) in yak follicular development and its regulatory mechanism remains unclear. To explore the differentially expressed lncRNAs between healthy and atretic follicular in yaks. We used RNA-seq to construct lncRNA, miRNA, and mRNA expression profiles in yak atretic and healthy follicles, and the RNA sequence results were identified by qPCR. In addition, the correlation of lncRNA and targeted mRNA was also analyzed by Starbase software. Moreover, lncRNA/miRNA/mRNA networks were constructed by Cytoscape software, and the network was verified by dual-luciferase analysis. A total of 682 novel lncRNAs, 259 bta-miRNAs, and 1704 mRNAs were identified as differentially expressed between healthy and atretic follicles. Among them, 135 mRNAs were positively correlated with lncRNA expression and 97 were negatively correlated, which may be involved in the yak follicular development. In addition, pathway enrichment analysis of differentially expressed lncRNA host genes by Kyoto Genome Encyclopedia (KEGG) showed that host genes were mainly involved in hormone secretion, granulosa cell apoptosis, and follicular development. In conclusion, we identified a series of novel lncRNAs, constructed the lncRNA ceRNA regulatory network, and provided comprehensive resources for exploring the role of lncRNAs in yak ovarian follicular development.
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Affiliation(s)
- Yilong Yao
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaoyi Meng
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Wangchang Li
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yefen Xu
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Yunlu Wang
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Sizhu Suolang
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Guangyin Xi
- College of Animal Sciences and Technology, China Agricultural University, Haidian, Beijing, China
| | - Lei Cao
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Min Guo
- College of Animal Sciences and Technology, China Agricultural University, Haidian, Beijing, China
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7
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Han H, Wang X, Li W, Liu J, Fan Y, Zhang H, Yang J, Gao Y, Liu Y. Identification and Characterization of lncRNAs Expression Profile Related to Goat Skeletal Muscle at Different Development Stages. Animals (Basel) 2022; 12:ani12192683. [PMID: 36230427 PMCID: PMC9558979 DOI: 10.3390/ani12192683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
LncRNAs are essential for regulating skeletal muscle. However, the expression profile and function of lncRNAs in goat muscle remains unclear. Here, an average of ~14.58 Gb high-quality reads were obtained from longissimus dorsi tissues of 1-month-old (n = 3) and 9-month-old (n = 3) Wu'an black goats using RNA sequencing. Of a total of 3441 lncRNAs, 1281 were lincRNAs, 805 were antisense lncRNAs, and 1355 were sense_overlapping lncRNAs. These lncRNAs shared some properties with goats, such as fewer exons, shorter transcript, and open reading frames (ORFs) length. Among them, 36 differentially expressed lncRNAs (DE lncRNA) were identified, and then 10 random lncRNAs were validated by RT-qPCR. Furthermore, 30 DE lncRNAs were neighboring 71 mRNAs and several genes were functionally enriched in muscle development-related pathways, such as APC, IFRD1, NKX2-5, and others. Additionally, 36 DE lncRNAs and 2684 mRNAs were included in co-expression interactions. A lncRNA-miRNA-mRNA network containing 4 lncRNAs, 3 miRNAs, and 8 mRNAs was finally constructed, of which XR_001296113.2 might regulate PDLIM7 expression by interaction with chi-miR-1296 to affect skeletal muscle development. This study revealed the expression profile of goat lncRNAs for further investigative studies and provides a fuller understanding of skeletal muscle development.
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Affiliation(s)
- Haiyin Han
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
| | - Xianwei Wang
- Henan Animal Husbandry Service, Zhengzhou 450046, China
| | - Wentao Li
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
| | - Jiannan Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056021, China
| | - Yekai Fan
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
| | - Hui Zhang
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
| | - Junqi Yang
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
| | - Yahui Gao
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
- Correspondence: (Y.G.); (Y.L.); Tel./Fax: +86-0310-8573021 (Y.G.); +86-0310-8573009 (Y.L.)
| | - Yufang Liu
- School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056021, China
- Correspondence: (Y.G.); (Y.L.); Tel./Fax: +86-0310-8573021 (Y.G.); +86-0310-8573009 (Y.L.)
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8
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Zhu CY, Zheng Q, Pan QQ, Jing J, Qin SQ, Lou MY, Yang YH, Wei JB, Li S, Fang FG, Liu Y, Ling YH. Analysis of lncRNA in the skeletal muscle of rabbits at different developmental stages. Front Vet Sci 2022; 9:948929. [PMID: 36213392 PMCID: PMC9533132 DOI: 10.3389/fvets.2022.948929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
It is universally acknowledged that lncRNA plays an important role in the regulation of animal skeletal muscle development regulation. However, there is a lack of relevant research on lncRNA in rabbit skeletal muscle development. Thus, we explored the expression profiles of lncRNA in rabbits at three growth stages (2-week-old fetus, 6-week-old post-weaning, and 6-month-old adult) using RNA-seq. A total of 554 differentially expressed lncRNAs (235 up- and 319 down-regulated) were found between the post-weaning and fetus groups and 19 (7 up- and 12 down-regulated) between the post-weaning and adult groups and 429 (115 up- and 314 down-regulated) between the fetus and adult. The enrichment pathways in the post-weaning and fetus groups were mainly concentrated at AMPK and PI3K-Akt signaling pathways, and the co-expression results revealed that LINC-2903, LINC-2374, LINC-8591 plays a role in early maintenance of skeletal muscle development. The enriched pathways in the fetus and adult groups were mainly involved in PI3K-Akt signaling pathways with a strong association found in mTOR signaling pathways. Analysis of the co-expression results suggests that LINC-5617 may be involved in the proliferation of embryonic skeletal muscle cells, and that LINC-8613 and LINC-8705 may provide energy for postnatal skeletal muscle development. The specific roles of different lncRNAs in different developmental stages of New Zealand White rabbits obtained. This will contribute to the subsequent study on the regulatory mechanism of muscle development in New Zealand White rabbits.
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Affiliation(s)
- Cuiyun Y. Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Qianqian Q. Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Jing Jing
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Shuaiqi Q. Qin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Mengyu Y. Lou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Yuhang H. Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Jinbo B. Wei
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Shuang Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Fugui G. Fang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
| | - Yong Liu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Yinghui H. Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, China
- *Correspondence: Yinghui H. Ling
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Resveratrol Inhibits Proliferation and Differentiation of Porcine Preadipocytes by a Novel LincRNA-ROFM/miR-133b/AdipoQ Pathway. Foods 2022; 11:foods11172690. [PMID: 36076875 PMCID: PMC9455634 DOI: 10.3390/foods11172690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Resveratrol (RES) has a wide range of biological and pharmacological activities with various health benefits for humans as a food additive. In animal production, RES has been considered a potential functional feed additive for producing high-quality pork. Long noncoding RNAs (lncRNAs) have emerged as essential regulators of fat metabolism, and phytochemicals can regulate fat metabolism through lncRNA. However, it is unclear whether RES can improve back-fat thickness by regulating lncRNA. In this study, we identified a novel lncRNA, which was named a long intergenic non-protein coding RNA, a regulator of fat metabolism (LincRNA-ROFM), from our previous lncRNA sequencing data. LincRNA-ROFM can inhibit adipocyte proliferation and differentiation. In-depth analyses showed that LincRNA-ROFM acts as a molecular sponge for miR-133b, and adiponectin (AdipoQ) is a direct target of miR-133b in porcine preadipocytes. In addition, the expression of LincRNA-ROFM was positively correlated with AdipoQ. RES can promote the expression of LincRNA-ROFM by PPARα and C/EBPα. Altogether, our research showed that LincRNA-ROFM acts as a ceRNA to sequester miR-133b and is upregulated by RES, leading to heightened AdipoQ expression, and thus decreased adipocyte proliferation and differentiation, which reduces back-fat thickness of pigs. Taken together, the RES/LincRNA-ROFM/miR-133b/AdipoQ regulatory network preliminarily explains the mechanism of action of RES in inhibiting fat deposition, which provides new insight into the downstream mechanism of RES inhibition of fat deposits by regulating the lncRNA.
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10
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Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens. Genes (Basel) 2022; 13:genes13061033. [PMID: 35741795 PMCID: PMC9222894 DOI: 10.3390/genes13061033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Chicken is the most widely consumed meat product worldwide and is a high-quality source of protein for humans. The skeletal muscle, which accounts for the majority of chicken products and contains the most valuable components, is tightly correlated to meat product yield and quality. In domestic chickens, skeletal muscle growth is regulated by a complex network of molecules that includes some non-coding RNAs (ncRNAs). As a regulator of muscle growth and development, ncRNAs play a significant function in the development of skeletal muscle in domestic chickens. Recent advances in sequencing technology have contributed to the identification and characterization of more ncRNAs (mainly microRNAs (miRNAs), long non-coding RNAs (LncRNAs), and circular RNAs (CircRNAs)) involved in the development of domestic chicken skeletal muscle, where they are widely involved in proliferation, differentiation, fusion, and apoptosis of myoblasts and satellite cells, and the specification of muscle fiber type. In this review, we summarize the ncRNAs involved in the skeletal muscle growth and development of domestic chickens and discuss the potential limitations and challenges. It will provide a theoretical foundation for future comprehensive studies on ncRNA participation in the regulation of skeletal muscle growth and development in domestic chickens.
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Liu R, Han M, Liu X, Yu K, Bai X, Dong Y. Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle. Front Genet 2022; 13:849399. [PMID: 35651943 PMCID: PMC9149217 DOI: 10.3389/fgene.2022.849399] [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: 01/06/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
There is an increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. In this study, the transcriptome numbers of longissimus muscle of different beef cattle (Shandong black catle and Luxi catlle) were used to construct muscle related lncRNAs-miRNA-mRNA interaction network through bioinformatics analysis. This is helpful to clarify the molecular mechanism of bovine muscle development, and can be used to promote animal husbandry and improve animal husbandry production. According to the screening criteria of |FC|≧2 and q < 0.05, a total of 1,415 transcripts (of which 480 were LncRNAs) were differentially expressed (q < 0.05) in the different breeds. Further, we found that the most differentially expressed LncRNAs were found on chromosome 9, in which the differentially expressed LncRNAs targeted 1,164 protein coding genes (MYORG, Wnt4, PAK1, ADCY7,etc) (upstream and downstream<50 Kb). In addition, Pearson’s correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may combined miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds.
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Affiliation(s)
- Ruili Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Mingxuan Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xianxun Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Kun Yu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xuejin Bai
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Yajuan Dong
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
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LncR-133a Suppresses Myoblast Differentiation by Sponging miR-133a-3p to Activate the FGFR1/ERK1/2 Signaling Pathway in Goats. Genes (Basel) 2022; 13:genes13050818. [PMID: 35627202 PMCID: PMC9141198 DOI: 10.3390/genes13050818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/30/2022] [Accepted: 05/01/2022] [Indexed: 12/03/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in a variety of biological processes and illnesses. While a considerable number of lncRNAs have been discovered in skeletal muscle to far, their role and underlying processes during myogenesis remain mostly unclear. In this study, we described a new functional lncRNA named lncR-133a. Gene overexpression and interference studies in goat skeletal muscle satellite cells (MuSCs) were used to establish its function. The molecular mechanism by which lncR-133a governs muscle differentiation was elucidated primarily using quantitative real-time PCR (qRT-PCR), Western blotting, dual-luciferase activity assays, RNA immunoprecipitation, biotin-labeled probe, and RNA fluorescence in situ hybridization analyses. LncR-133a was found to be substantially expressed in longissimus thoracis et lumborum muscle, and its expression levels changed during MuSC differentiation in goats. We validated that lncR-133a suppresses MuSC differentiation in vitro. Dual-luciferase reporter screening, Argonaute 2 (AGO2) RNA immunoprecipitation assays, biotin-labeled lncR-133a capture, and fluorescence in situ hybridization showed that lncR-133a interacted with miR-133a-3p. Additionally, miR-133a-3p facilitated MuSC differentiation, but lncR-133a reversed this effect. The luciferase reporter assay and functional analyses established that miR-133a-3p directly targets fibroblast growth factor receptor 1 (FGFR1). Moreover, lncR-133a directly reduced miR-133a-3p’s capacity to suppress FGFR1 expression, and positively regulated the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). In summary, our results suggested that lncR-133a suppresses goat muscle differentiation by targeting miR-133a-3p and activating FGFR1/ERK1/2 signaling pathway.
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Knockdown of CDR1as Decreases Differentiation of Goat Skeletal Muscle Satellite Cells via Upregulating miR-27a-3p to Inhibit ANGPT1. Genes (Basel) 2022; 13:genes13040663. [PMID: 35456469 PMCID: PMC9026999 DOI: 10.3390/genes13040663] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 02/01/2023] Open
Abstract
Myogenesis is a complex process controlled by several coding and non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) that are known to function as endogenous microRNAs (miRNAs) sponges. Cerebellar Degeneration-Related protein 1 antisense (CDR1as) is the most spotlighted circRNA that is known as an miR-7 sponge, which has bloomed circRNAs’ research in animal disease and physiology. Here, we screened for miRNAs and mRNA associated with CDR1as and further characterized their regulatory function during muscle differentiation. We found that a total of 43 miRNAs (including miR-107-3p, miR-125b-5p, miR-140-5p, miR-29a-3p, and miR-27a-3p upregulated) and 789 mRNAs (including ANGPT1, E2F2, CCN1, FGFR1, and MEF2C downregulated) were differentially expressed in goat skeletal muscle satellite cells (SMSCs). Further, knockdown of CDR1as and ANGPT1 inhibited SMSCs differentiation. miR-27a-3p was differentially upregulated after the knockdown of CDR1as in SMSCs. Overexpressed miR-27a-3p decreased SMSCs differentiation. Via RNAhybrid and luciferase, miR-27a-3p was identified to regulate ANGPT1. We discovered that miR-27a-3p has an inverse relationship with CDR1as and decreases the expression level of ANGPT1 during SMSCs differentiation. In summary, our study demonstrates that siCDR1as inhibits myoblast differentiation by downregulating ANGPT1 mRNA via miR-27a-3p in SMSCs.
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Ye J, Zhao X, Xue H, Zou X, Liu G, Deng M, Sun B, Guo Y, Liu D, Li Y. RNA-Seq Reveals miRNA and mRNA Co-regulate Muscle Differentiation in Fetal Leizhou Goats. Front Vet Sci 2022; 9:829769. [PMID: 35400087 PMCID: PMC8990838 DOI: 10.3389/fvets.2022.829769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Muscle differentiation is an essential link in animal growth and development, and microRNA and mRNA are indispensable in skeletal muscle differentiation. To improve the meat quality and production of the Leizhou goat, it is vital to understand the molecular mechanism by which its skeletal muscle differentiates. By RNA sequencing (RNA-SEQ), we established miRNA-mRNA profiles of Leizhou goats at three stages: fetal day 70, 90, and 120. There were 991 differently expressed mRNAs and 39 differentially expressed miRNAs found, with the differentially expressed mRNAs mainly enriched in calcium ion binding, ECM-receptor interaction, and Focal adhesion. CKM and MYH3, two muscle differentiation markers, were significantly differentially expressed during this period. In addition, we found that chi-miR-129-5p, chi-miR-433, and chi-miR-24-3p co-regulate muscle differentiation with their target genes. Finally, we can confirm that muscle differentiation occurred in Leizhou goat between 90 and 120 days of the fetus. This study is helpful to better explore the molecular mechanism of goat muscle differentiation.
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Affiliation(s)
- Junning Ye
- College of Animal Science, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Xiuhui Zhao
- College of Animal Science, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Huiwen Xue
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
- *Correspondence: Yaokun Li
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Yang Y, Wang Y, Shan H, Zheng Y, Xuan Z, Hu J, Wei M, Wang Z, Liu Q, Li Z. Novel Insights into the Differences in Nutrition Value, Gene Regulation and Network Organization between Muscles from Pasture-Fed and Barn-Fed Goats. Foods 2022; 11:foods11030381. [PMID: 35159531 PMCID: PMC8834483 DOI: 10.3390/foods11030381] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/04/2022] Open
Abstract
The physiological and biochemical characters of muscles derived from pasture-fed or barn-fed black goats were detected, and RNA-seq was performed to reveal the underlying molecular mechanisms to identify how the pasture feeding affected the nutrition and flavor of the meat. We found that the branched chain amino acids, unsaturated fatty acids, and zinc in the muscle of pasture-fed goats were significantly higher than those in the barn-fed group, while the heavy metal elements, cholesterol, and low-density lipoprotein cholesterol were significantly lower. RNA-seq results showed that 1761 genes and 147 lncRNA transcripts were significantly differentially expressed between the pasture-fed and barn-fed group. Further analysis found that the differentially expressed genes were mainly enriched in the myogenesis and Glycerophospholipid metabolism pathway. A functional analysis of the lncRNA transcripts further highlighted the difference in fatty acid metabolism between the two feeding models. Our study provides novel insights into the gene regulation and network organization of muscles and could be potentially used for improving the quality of mutton.
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Affiliation(s)
- Yufeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Yan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Huiquan Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Yalin Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Zeyi Xuan
- The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530010, China; (Z.X.); (M.W.)
| | - Jinling Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Mingsong Wei
- The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530010, China; (Z.X.); (M.W.)
| | - Zhiqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.Y.); (Y.W.); (H.S.); (Y.Z.); (J.H.); (Z.W.); (Q.L.)
- Correspondence:
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16
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Huang CN, Liu CL, Zeng SQ, Liu CB, Si WJ, Yuan Y, Ren LX, He YM, Zhang WY, Zhang HY, Zeng Y, Han YG, Na RS, Ee GX, Huang YF. Identification of differentially expressed long non-coding RNAs and messenger RNAs involved with muscle development in Dazu black goats through RNA sequencing. Anim Biotechnol 2022:1-9. [PMID: 34985384 DOI: 10.1080/10495398.2021.2020804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This study aimed to explore the genetic basis of muscle development in goats. The transcriptome dataset for differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) of goat muscle at different developmental stages were obtained using RNA-Seq. A total of 447,806,481 and 587,559,465 clean reads in the longissimus dorsi muscle of Dazu black goats between 75d embryonic stage and 1d after birth were generated through Illumina paired-end sequencing, and their mapping rates were 89.82 and 90.99%, respectively. Moreover, 4517 DEGs and 648 DELs were identified, and 4784 lncRNA-mRNA targeting relationships were predicted. Gene function annotation results showed that 4101 DEGs were significantly enriched to 1098 GO terms, and 2014 DEGs were significantly enriched to 40 KEGG pathways, including many GO terms and pathways related to muscle development, such as cell differentiation and Wnt signaling pathway. Then, 10 DELs and 20 DEGs were randomly selected for RT-qPCR verification, and the agreement rate between the verification and RNA-Seq results was 90%, indicating the high reliability of the RNA-Seq data analysis. In conclusion, this study obtained several mRNAs and lncRNAs related to the muscle development of Dazu black goats and identified several targeted regulatory pairs of lncRNA-mRNA. This study may serve as a reference to understand the genetic basis and molecular mechanism of muscle development in goats.
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Affiliation(s)
- Chao-Nan Huang
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Cheng-Li Liu
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Shi-Qi Zeng
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Chang-Bao Liu
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Wei-Jiang Si
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Ying Yuan
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Li-Xin Ren
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Meng He
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Wei-Yi Zhang
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Hao-Yuan Zhang
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Zeng
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan-Guo Han
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Ri-Su Na
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Guang-Xin Ee
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yong-Fu Huang
- Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, College of Animal Science and Technology, Southwest University, Chongqing, China
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Zhang X, Bao P, Ye N, Zhou X, Zhang Y, Liang C, Guo X, Chu M, Pei J, Yan P. Identification of the Key Genes Associated with the Yak Hair Follicle Cycle. Genes (Basel) 2021; 13:genes13010032. [PMID: 35052373 PMCID: PMC8774716 DOI: 10.3390/genes13010032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
The development of hair follicles in yak shows significant seasonal cycles. In our previous research, transcriptome data including mRNAs and lncRNAs in five stages during the yak hair follicles (HFs) cycle were detected, but their regulation network and the hub genes in different periods are yet to be explored. This study aimed to screen and identify the hub genes during yak HFs cycle by constructing a mRNA-lncRNA co-expression network. A total of 5000 differently expressed mRNA (DEMs) and 729 differently expressed long noncoding RNA (DELs) were used to construct the co-expression network, based on weighted genes co-expression network analysis (WGCNA). Four temporally specific modules were considered to be significantly associated with the HFs cycle of yak. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the modules are enriched into Wnt, EMC-receptor interaction, PI3K-Akt, focal adhesion pathways, and so on. The hub genes, such as FER, ELMO1, PCOLCE, and HOXC13, were screened in different modules. Five hub genes (WNT5A, HOXC13, DLX3, FOXN1, and OVOL1) and part of key lncRNAs were identified for specific expression in skin tissue. Furthermore, immunofluorescence staining and Western blotting results showed that the expression location and abundance of DLX3 and OVOL1 are changed following the process of the HFs cycle, which further demonstrated that these two hub genes may play important roles in HFs development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ping Yan
- Correspondence: ; Tel.: +86-0931-2115288
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Wang D, Pu Y, Li Y, Pan D, Wang S, Tian W, Ma Y, Jiang L. Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs. BMC Genomics 2021; 22:593. [PMID: 34348644 PMCID: PMC8340374 DOI: 10.1186/s12864-021-07881-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The mutation of insulin-like growth factor 2 (IGF2 mutation) that a single-nucleotide substitution (G→A) in the third intron of IGF2 abrogates the interaction with zinc finger BED-type containing 6 (ZBED6) and leads to increased muscle mass in pigs. IGF2 mutation knock-in (IGF2 KI) and ZBED6 knockout (ZBED6 KO) lead to changes in IGF2 expression and increase muscle mass in mice and pigs. Long noncoding RNAs (lncRNAs) may participate in numerous biological processes, including skeletal muscle development. However, the role of the ZBED6-lncRNA axis in skeletal muscle development is poorly characterized. RESULTS In this study, we assembled transcriptomes using RNA-seq data published in previous studies by our group and identified 11,408 known lncRNAs and 2269 potential lncRNAs in seven tissues, heart, longissimus dorsi, gastrocnemius muscle, liver, spleen, lung and kidney, of ZBED6 KO (lean mass model) and WT Bama pigs. ZBED6 affected the expression of 1570 lncRNAs (differentially expressed lncRNAs [DE-lncRNAs]; log2-fold change ≥ 1, nominal p-value ≤ 0.05) in the seven examined tissues. The expressed lncRNAs (FPKM > 0.1) exhibited tissue-specific patterns in WT pigs. Specifically, 3410 lncRNAs were expressed exclusively in only one tissue. Potential functions of lncRNAs were indirectly predicted by searching their target cis- and trans-regulated protein-coding genes. LncRNAs with tissue-specific expression influence numerous genes related to tissue functions. Weighted gene coexpression network analysis (WGCNA) of 1570 DE-lncRNAs between WT and ZBED6 KO pigs was used to define the following six lncRNA modules specific to different tissues: skeletal muscle, heart, lung, spleen, kidney and liver modules. Furthermore, by conjoint analysis of longissimus dorsi data (tissue-specific expression, muscle module and DE-lncRNAs) and ChIP-PCR revealed NONSUSG002145.1 (adjusted p-values = 0.044), which is coexpressed with the IGF2 gene and binding with ZBED6, may play important roles in ZBED6 KO pig skeletal muscle development. CONCLUSIONS These findings indicate that the identified lncRNAs may play essential roles in tissue function and regulate the mechanism of ZBED6 action in skeletal muscle development in pigs. To our knowledge, this is the first study describing lncRNAs in ZBED6 KO pigs. These results may open new research directions leading to a better understanding of the global functions of ZBED6 and of lncRNA functions in skeletal muscle development in pigs.
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Affiliation(s)
- Dandan Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Yabin Pu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Yefang Li
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Dengke Pan
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.,Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, 610072, Chengdu, China
| | - Shengnan Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Wenjie Tian
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China. .,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China. .,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.
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19
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Jing J, Jiang X, Zhu C, Zheng Q, Ji Q, Yin H, Huang J, Zhu Y, Wang J, Qin S, Ling Y. Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits. BMC Genomics 2021; 22:577. [PMID: 34315409 PMCID: PMC8314457 DOI: 10.1186/s12864-021-07896-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND miRNA is one of the crucial roles in the complex and dynamic network that regulates the development of skeletal muscle. The landscape of skeletal muscle miRNAs from fetus to adult in New Zealand rabbits has not been revealed yet. RESULTS In this study, nine RNA-seq libraries of fetus, child and adult rabbits' leg muscles were constructed. A total of 278 differentially expressed miRNAs (DEmiRNAs) were identified. In the fetus vs. child group, the main functional enrichments were involved in membrane and transport. Pathway enriched terms of up-regulated DEmiRNAs were connected with the differentiation and hypertrophy of skeletal muscle, and down-regulated ones were related to muscle structure and metabolic capacity. In the child vs. adult group, functions were associated to positioning and transportation, and pathways were relevant to ECM, muscle structure and hypertrophy. Finally, ocu-miR-185-3p and ocu-miR-370-3p, which had the most target genes, were identified as hub-miRNAs in these two groups. CONCLUSIONS In short, we summarized the highly expressed and uniquely expressed DEmiRNAs of fetus, child and adult rabbits' leg muscles. Besides, the potential functional changes of miRNAs in two consecutive stages have been explored. Among them, the ocu-miR-185-3p and ocu-miR-370-3p with the most target genes were selected as hub-miRNAs. These data improved the understanding of the regulatory molecules of meat rabbit development, and provided a novel perspective for molecular breeding of meat rabbits.
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Affiliation(s)
- Jing Jing
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Xichun Jiang
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui, 230031, Hefei, People's Republic of China
| | - Cuiyun Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Qianyun Ji
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Huiqun Yin
- Reproductive Medicine Center, The 901st Hospital, Anhui, 230031, Hefei, People's Republic of China
| | - Jingtong Huang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Yixiao Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Jiao Wang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Shuaiqi Qin
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China. .,Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio- Breeding, Anhui Agricultural University, Anhui, 230036, Hefei, People's Republic of China.
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20
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Chitneedi PK, Weikard R, Arranz JJ, Martínez-Valladares M, Kuehn C, Gutiérrez-Gil B. Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep. Front Genet 2021; 12:685341. [PMID: 34194481 PMCID: PMC8236958 DOI: 10.3389/fgene.2021.685341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Several recent studies have demonstrated the role of long non-coding RNAs (lncRNAs) in regulating the defense mechanism against parasite infections, but no studies are available that investigated their relevance for immune response to nematode infection in sheep. Thus, the aim of the current study was to (i) detect putative lncRNAs that are expressed in the abomasal lymph node of adult sheep after an experimental infection with the gastrointestinal nematode (GIN) Teladorsagia circumcincta and (ii) to elucidate their potential functional role associated with the differential host immune response. We hypothesized that putative lncRNAs differentially expressed (DE) between samples from animals that differ in resistance to infection may play a significant regulatory role in response to nematode infection in adult sheep. To obtain further support for our hypothesis, we performed co-expression and functional gene enrichment analyses with the differentially expressed lncRNAs (DE lncRNAs). In a conservative approach, we included for this predictive analysis only those lncRNAs that are confirmed and supported by documentation of expression in gastrointestinal tissues in the current sheep gene atlas. We identified 9,105 putative lncRNA transcripts corresponding to 7,124 gene loci. Of these, 457 were differentially expressed lncRNA loci (DELs) with 683 lncRNA transcripts. Based on a gene co-expression analysis via weighted gene co-expression network analysis, 12 gene network modules (GNMs) were found significantly correlated with at least one of 10 selected target DE lncRNAs. Based on the principle of “guilt-by-association,” the DE genes from each of the three most significantly correlated GNMs were subjected to a gene enrichment analysis. The significant pathways associated with DE lncRNAs included ERK5 Signaling, SAPK/JNK Signaling, RhoGDI Signaling, EIF2 Signaling, Regulation of eIF4 and p70S6K Signaling and Oxidative Phosphorylation pathways. They belong to signaling pathway categories like Cellular Growth, Proliferation and Development, Cellular Stress and Injury, Intracellular and Second Messenger Signaling and Apoptosis. Overall, this lncRNA study conducted in adult sheep after GIN infection provided first insights into the potential functional role of lncRNAs in the differential host response to nematode infection.
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Affiliation(s)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - María Martínez-Valladares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain.,Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Christa Kuehn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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21
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Systematic Analysis of Long Noncoding RNA and mRNA in Granulosa Cells during the Hen Ovulatory Cycle. Animals (Basel) 2021; 11:ani11061533. [PMID: 34070248 PMCID: PMC8225051 DOI: 10.3390/ani11061533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Chicken is one of the most economically important farm poultry, and providing many food products, such as meat and eggs for human consumption. However, follicle transcriptome studies in chickens with timepoints relating to changes in luteinizing hormone level remain unknown. In this study, the largest preovulatory follicle of chicken underwent the early, middle, and terminal stages of ovulatory cycle. Our work provides a comprehensive analysis of lncRNAs and mRNAs in chicken granulosa cells during the ovulatory cycle. A total of 12,479 mRNAs and 7528 lncRNAs were identified among the three stages. Thousands of lncRNAs were annotated, and the most differentially abundant genes were detected in the luteinizing hormone surge stage. Functional features of the lncRNAs and mRNAs at each stage were revealed, which was also associated with the changes in serum luteinizing hormone level. Especially, genes related to oxidative stress, steroids regulation, and inflammatory process were enriched in the luteinizing hormone surge stage, The comprehensive data generated in this study provides the foundation for future investigations to improve the reproductive performance of chickens and explore the mechanisms responsible for female ovarian diseases. Abstract Long non-coding RNAs (lncRNAs) and mRNAs are temporally expressed during chicken follicle development. However, follicle transcriptome studies in chickens with timepoints relating to changes in luteinizing hormone (LH) levels are rare. In this study, gene expression in Rohman layers was investigated at three distinct stages of the ovulatory cycle: zeitgeber time 0 (ZT0, 9:00 a.m.), zeitgeber time 12 (ZT12, 9:00 p.m.), and zeitgeber time 20 (ZT20, 5:00 a.m.) representing the early, middle, and LH surge stages, respectively, of the ovulatory cycle. Gene expression profiles were explored during follicle development at ZT0, ZT12, and ZT20 using Ribo-Zero RNA sequencing. The three stages were separated into two major stages, including the pre-LH surge and the LH surge stages. A total of 12,479 mRNAs and 7528 lncRNAs were identified among the three stages, and 4531, 523 differentially expressed genes (DEGs) and 2367, 211 differentially expressed lncRNAs (DELs) were identified in the ZT20 vs. ZT12, and ZT12 vs. ZT0, comparisons. Functional enrichment analysis revealed that genes involved in cell proliferation and metabolism processes (lipid-related) were mainly enriched in the ZT0 and ZT12 stages, respectively, and genes related to oxidative stress, steroids regulation, and inflammatory process were enriched in the ZT20 stage. These findings provide the basis for further investigation of the specific genetic and molecular functions of follicle development in chickens.
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22
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Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA). Animals (Basel) 2021; 11:ani11020314. [PMID: 33513831 PMCID: PMC7911360 DOI: 10.3390/ani11020314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/23/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In the past few years, studies on the gene expression changes of dairy cow mammary glands were only based on transcriptome comparisons between two lactation stages. Few studies focused on the relationships between gene expression of the dairy mammary gland and lactation stage or milk composition in a lactation cycle. In this study, we detected milk yield and composition in a lactation cycle. For the first time, we constructed a gene coexpression network using WGCNA on the basis of 18 gene expression profiles during six stages of a lactation cycle by transcriptome sequencing, generating 10 specific modules. Genes in each module were performed with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Module–trait relationship analysis showed a series of potential candidates related to milk yield and composition. The current study provides an important theoretical basis for the further molecular breeding of dairy cows. Abstract Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In this study, the milk yield, lactose, fat, and protein of Holstein dairy cows were detected in a lactation cycle. Meanwhile, a total of 18 gene expression profiles were detected using mammary glands from six lactation stages (day 7 to calving, −7 d; day 30 post-calving, 30 d; day 90 post-calving, 90 d; day 180 post-calving, 180 d; day 270 post-calving, 270 d; day 315 post-calving, 315 d). On the basis of the 18 profiles, WGCNA identified for the first time 10 significant modules that may be related to lactation stage, milk yield, and the main milk composition content. Genes in the 10 significant modules were examined with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results revealed that the galactose metabolism pathway was a potential candidate for milk yield and milk lactose synthesis. In −7 d, ion transportation was more frequent and cell proliferation related terms became active. In late lactation, the suppressor of cytokine signaling 3 (SOCS3) might play a role in apoptosis. The sphingolipid signaling pathway was a potential candidate for milk fat synthesis. Dairy cows at 315 d were in a period of cell proliferation. Another notable phenomenon was that nonlactating dairy cows had a more regular circadian rhythm after a cycle of lactation. The results provide an important theoretical basis for the further molecular breeding of dairy cows.
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23
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Tan Y, Gan M, Shen L, Li L, Fan Y, Chen Y, Chen L, Niu L, Zhao Y, Jiang A, Jiang D, Zhang S, Zhu L. Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development. Int J Mol Sci 2021; 22:ijms22020503. [PMID: 33419093 PMCID: PMC7825455 DOI: 10.3390/ijms22020503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 11/16/2022] Open
Abstract
Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.
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Affiliation(s)
- Ya Tan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, China
| | - Yuan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Ying Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Anan Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Dongmei Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Shunhua Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Correspondence: (S.Z.); (L.Z.); Tel.: +86-28-8629-1133 (S.Z. & L.Z.)
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Correspondence: (S.Z.); (L.Z.); Tel.: +86-28-8629-1133 (S.Z. & L.Z.)
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Fu X, Zhao B, Tian K, Wu Y, Suo L, Ba G, Ciren D, De J, Awang C, Gun S, Yang B. Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PeerJ 2020; 8:e10217. [PMID: 33240606 PMCID: PMC7659624 DOI: 10.7717/peerj.10217] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
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Affiliation(s)
- Xuefeng Fu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingru Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kechuan Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Gui Ba
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Deji Ciren
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Ji De
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Cuoji Awang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bohui Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
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