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Zhu J, Wang Y, Su Y, Zheng M, Cui H, Chen Z. RNA sequencing identifies key genes involved in intramuscular fat deposition in chickens at different developmental stages. BMC Genomics 2024; 25:219. [PMID: 38413888 PMCID: PMC10900564 DOI: 10.1186/s12864-023-09819-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: 07/04/2023] [Accepted: 11/20/2023] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Intramuscular fat (IMF) is an important factor in meat quality, and triglyceride (TG) and Phospholipids (PLIP), as the main components of IMF, are of great significance to the improvement of meat quality. RESULTS In this study, we used 30 RNA sequences generated from the transcriptome of chicken breast muscle tissues at different developmental stages to construct a gene expression matrix to map RNA sequence reads to the chicken genome and identify the transcript of origin. We used weighted gene co-expression network analysis (WGCNA) and identified 27 co-expression modules, 10 of which were related to TG and PLIP. We identified 150 highly-connected hub genes related to TG and PLIP, respectively, which were found to be mainly enriched in the adipocytokine signaling pathway, MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, and TGF-beta signaling pathway. Additionally, using the BioMart database, we identified 134 and 145 candidate genes related to fat development in the TG-related module and PLIP-related module, respectively. Among them, RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 were identified as candidate genes related to fat development and highly-connected hub genes in the module, suggesting that these ten genes may be important candidate genes affecting IMF deposition. CONCLUSIONS RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 may be important candidate genes affecting IMF deposition. The purpose of this study was to identify the co-expressed gene modules related to chicken IMF deposition using WGCNA and determine key genes related to IMF deposition, so as to lay a foundation for further research on the molecular regulation mechanism underlying chicken fat deposition.
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Affiliation(s)
- Jinmei Zhu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yongli Wang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yongchun Su
- Guangxi Jingling Agriculture and animal Husbandry Group Co., LTD, Nanning, 530049, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huanxian Cui
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zhiwu Chen
- Guangxi Jingling Agriculture and animal Husbandry Group Co., LTD, Nanning, 530049, China.
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Chen G, Lin Z, Peng H, Zhang S, Zhang Z, Zhang X, Nie Q, Luo W. The transmembrane protein TMEM182 promotes fat deposition and alters metabolomics and lipidomics. Int J Biol Macromol 2024; 259:129144. [PMID: 38181918 DOI: 10.1016/j.ijbiomac.2023.129144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/10/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
TMEM182, a transmembrane protein highly expressed in muscle and adipose tissues, plays a crucial role in muscle cell differentiation, metabolism, and signaling. However, its role in fat deposition and metabolism is still unknown. In this study, we used overexpression and knockout models to examine the impact of TMEM182 on fat synthesis and metabolism. Our results showed that TMEM182 overexpression increased the expression of fat synthesis-related genes and promoted the differentiation of preadipocytes into fat cells. In TMEM182 knockout mice, there was a significant decrease in abdominal fat deposition. RNA sequencing results showed that TMEM182 overexpression in preadipocytes enhanced the activity of pathways related to fat formation, ECM-receptor interaction, and cell adhesion. Furthermore, our analysis using UPLC-MS/MS showed that TMEM182 significantly altered the metabolite and lipid content and composition in chicken breast muscle. Specifically, TMEM182 increased the content of amino acids and their derivatives in chicken breast muscle, promoting amino acid metabolic pathways. Lipidomics also revealed a significant increase in the content of glycerophospholipids, sphingolipids, and phospholipids in the breast muscle after TMEM182 overexpression. These findings suggest that TMEM182 plays a crucial role in regulating fat deposition and metabolism, making it a potential target for treating obesity-related diseases and animal breeding.
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Affiliation(s)
- Genghua Chen
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zetong Lin
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Haoqi Peng
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Shuai Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zihao Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong 510642, China; State Key Laboratory of Livestock and Poultry Breeding, Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Li J, Huang Q, Yang C, Yu C, Zhang Z, Chen M, Ren P, Qiu M. Molecular Regulation of Differential Lipid Molecule Accumulation in the Intramuscular Fat and Abdominal Fat of Chickens. Genes (Basel) 2023; 14:1457. [PMID: 37510361 PMCID: PMC10379444 DOI: 10.3390/genes14071457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Reducing abdominal fat (AF) accumulation and increasing the level of intramuscular fat (IMF) simultaneously is a major breeding goal in the poultry industry. To explore the different molecular mechanisms underlying AF and IMF, gene expression profiles in the breast muscle (BM) and AF from three chicken breeds were analyzed. A total of 4737 shared DEGs were identified between BM and AF, of which 2602 DEGs were upregulated and 2135 DEGs were downregulated in the BM groups compared with the AF groups. DEGs involved in glycerophospholipid metabolism and glycerolipid metabolism were potential regulators, resulting in the difference in lipid metabolite accumulation between IMF and AF. The PPAR signaling pathway was the most important pathway involved in tissue-specific lipid deposition. Correlation analysis showed that most representative DEGs enriched in the PPAR signaling pathway, such as FABP5, PPARG, ACOX1, and GK2, were negatively correlated with PUFA-enriched glycerophospholipid molecules. Most DEGs related to glycerophospholipid metabolism, such as GPD2, GPD1, PEMT, CRLS1, and GBGT1, were positively correlated with glycerophospholipid molecules, especially DHA- and arachidonic acid (ARA)-containing glycerophospholipid molecules. This study elucidated the molecular mechanism underlying tissue-specific lipid deposition and poultry meat quality.
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Affiliation(s)
- Jingjing Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Qinke Huang
- Guangyuan City Animal Husbandry Seed Management Station, Guangyuan 628107, China
| | - Chaowu Yang
- Sichuan Animal Science Academy, Chengdu 610066, China
| | - Chunlin Yu
- Sichuan Animal Science Academy, Chengdu 610066, China
| | | | - Meiying Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Peng Ren
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Mohan Qiu
- Sichuan Animal Science Academy, Chengdu 610066, China
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Li J, Li Z, Ran J, Yang C, Lin Z, Liu Y. LC/MS-based lipidomics to characterize breed-specific and tissue-specific lipid composition of chicken meat and abdominal fat. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wang L, Leng L, Ding R, Gong P, Liu C, Wang N, Li H, Du ZQ, Cheng B. Integrated transcriptome and proteome analysis reveals potential mechanisms for differential abdominal fat deposition between divergently selected chicken lines. J Proteomics 2021; 241:104242. [PMID: 33901680 DOI: 10.1016/j.jprot.2021.104242] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022]
Abstract
Genetic selection for meat production performance of broilers concomitantly causes excessive abdominal fat deposition, accompanied by several adverse effects, such as the reduction of feed conversion efficiency and reproduction performance. Our previous studies have identified important genes regulating chicken fat deposition, using the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) as an animal model. However, the molecular mechanism underlying fat deposition differences between fat and lean broilers remains largely unknown. Here, we integrated the transcriptome (RNA-Seq) and quantitative proteome (isobaric tags for relative and absolute quantitation, iTRAQ) profiling analyses on abdominal fat tissues from NEAUHLF chicken lines. Differentially expressed genes (2167 DEGs, corrected p-value < 0.01) and differentially abundant proteins (199 DAPs, corrected p-value < 0.05) were identified in lean line compared to fat line. Down-regulated DEGs and DAPs mainly enriched in pathways related to fatty acid metabolism, fatty acid biosynthesis, and PPAR signaling, and interestingly, up-regulated DEGs and DAPs enriched both in lysosome pathway. Moreover, numerous key DEGs and DAPs involved in long-chain fatty acid uptake, in situ lipogenesis (fatty acid and cholesterol synthesis), and lipid droplet accumulation were discovered after integrated transcriptome and proteome analysis. SIGNIFICANCE: Excessive abdominal fat deposition critically affects the health of broilers and causes economic loss to broiler producers, but the molecular mechanism of abdominal fat deposition is still unclear in chicken. We identified key DEGs/DAPs and potential pathways through an integration of chicken abdominal fat tissues transcriptome and proteome analyses. Our findings will facilitate a better revealing the mechanism and provide a novel insight into abdominal fat content discrepancy between the fat and lean chicken lines.
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Affiliation(s)
- Lijian Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Ran Ding
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Pengfei Gong
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Chang Liu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
| | - Bohan Cheng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, PR China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, PR China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
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6
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Transcriptome landscapes of differentially expressed genes related to fat deposits in Nandan-Yao chicken. Funct Integr Genomics 2021; 21:113-124. [PMID: 33404913 DOI: 10.1007/s10142-020-00764-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023]
Abstract
Nandan-Yao chicken is a Chinese native chicken with lower fat deposition and better meat quality. Fat deposition is a quite complex and important economic trait. However, its molecular mechanism is still unknown in chickens. In the current study, Nandan-Yao chicken was divided into two groups based on the rate of abdominal fat at 120 days old, namely the high-fat group and low-fat group. The total RNAs were isolated and sequenced by RNA sequencing (RNA-seq). After quality control, we gained 1222, 902, 784, 624, and 736 differentially expressed genes (DEGs) in abdominal fat, back skin, liver, pectoral muscle, and leg muscle, respectively. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that significantly enriched GO term and KEGG signaling pathway mainly involved cytosolic ribosome, growth development, PPAR signaling pathway, Wnt signaling pathway, and linoleic acid metabolism in abdominal fat, back skin, and liver. While in pectoral muscle and leg muscle, it is mainly enriched in phosphatidylinositol signaling system, adrenergic signaling in cardiomyocytes, cytosolic ribosome, and cytosolic part. Sixteen genes were differentially expressed in all five tissues. Among them, PLA2G4A and RPS4Y1 might be the key regulators for fat deposition in Nandan-Yao chicken. The protein-protein interaction (PPI) network analysis of DEGs showed that PCK1 was the most notable genes. The findings in the current study will help to understand the regulation mechanism of abdominal fat and intramuscular fat in Nandan-Yao chicken and provide a theoretical basis for Chinese local chicken breeding.
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Identification of Differentially Expressed Genes and Lipid Metabolism Signaling Pathways between Muscle and Fat Tissues in Broiler Chickens. J Poult Sci 2021; 58:131-137. [PMID: 33927567 PMCID: PMC8076620 DOI: 10.2141/jpsa.0200040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In this study, signaling pathways and key differentially expressed genes (DEGs) involved in lipid metabolism in muscle and fat tissues were investigated. Muscle and abdominal fat tissues were obtained from 35-day-old female broilers for RNA sequencing. DEGs between muscle and fat tissues were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of DEGs were performed. A total of 6130 DEGs were identified to be significantly enriched in 365 GO terms, most of which were involved in biological processes, cellular components, and molecular functions in muscle and fat tissues. Three important lipid signaling pathways (pyruvate metabolism, the insulin signaling pathway, and the adipocytokine signaling pathway) were identified among the fat and muscle tissues of broilers. The key common DEGs in these pathways included phosphoenolpyruvate carboxykinase 2 (PCK2), acetyl-CoA carboxylase 1 alpha and beta (ACACA and ACACB), and the mitogen-activated protein kinase (AMPK) gene family. Hence, our findings revealed the pathways and key genes and gene families involved in the regulation of fat deposition in the muscle and fat tissues of broilers.
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Zhang M, Ma X, Zhai Y, Zhang D, Sui L, Li W, Jiang R, Han R, Li G, Li Z, Wang Y, Tian Y, Kang X, Sun GR. Comprehensive Transcriptome Analysis of lncRNAs Reveals the Role of lncAD in Chicken Intramuscular and Abdominal Adipogenesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3678-3688. [PMID: 32125837 DOI: 10.1021/acs.jafc.9b07405] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Adipose tissue-specific distribution and deposition speed are the main factors affecting the slaughter performance and meat quality in poultry. Previous studies suggested that different adipose tissues owned various biochemical characteristics and gene expression patterns. To investigate the functional role of long noncoding RNAs (lncRNAs) during chicken intramuscular and abdominal adipogenesis, we performed transcriptome analysis by Ribo-Zero RNA-Seq technology. A total of 11247 lncRNAs were observed in the adipocytes derived from IMF and AbF in chicken. Among them, we got 1624 differentiated expressed novel lncRNAs. A large amount of lncRNAs were involved in several lipid metabolism and adipogenesis-related signaling pathways. Of these, lncRNAs, lncAD is one of the most upregulated lncRNA and was coexpressed with several genes of the PPAR signaling pathway. Here, we report that knockdown of lncAD inhibited its upstream gene TXNRD1 expression in a cis-regulation manner, thus to decrease intramuscular preadipocytes adipogenic differentiation and promoted cell proliferation. Our present study revealed huge lncRNAs profile differences between IMF- and AbF-derived preadipocyte adipogenesis. Collectively, our findings not only provide valuable evidence for the identification of adipogenic lncRNAs but also contribute to further studies about the post-transcriptional regulation mechanism underlying tissue-specific fat deposition in poultry.
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Affiliation(s)
- Meng Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Xiangfei Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Yanhui Zhai
- The First Hospital, Jilin University, Changchun 130021, Jilin P. R. China
| | - Daoyu Zhang
- The First Hospital, Jilin University, Changchun 130021, Jilin P. R. China
| | - Liyan Sui
- The First Hospital, Jilin University, Changchun 130021, Jilin P. R. China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
| | - Gui-Rong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan P. R. China
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Liu J, Lei Q, Li F, Zhou Y, Gao J, Liu W, Han H, Cao D. Dynamic Transcriptomic Analysis of Breast Muscle Development From the Embryonic to Post-hatching Periods in Chickens. Front Genet 2020; 10:1308. [PMID: 31998367 PMCID: PMC6967404 DOI: 10.3389/fgene.2019.01308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/27/2019] [Indexed: 11/30/2022] Open
Abstract
Skeletal muscle development and growth are closely associated with efficiency of poultry meat production and its quality. We performed whole transcriptome profiling based on RNA sequencing of breast muscle tissue obtained from Shouguang chickens at embryonic days (E) 12 and 17 to post-hatching days (D) 1, 14, 56, and 98. A total of 9,447 differentially expressed genes (DEGs) were filtered (Q < 0.01, fold change > 2). Time series expression profile clustering analysis identified five significantly different expression profiles that were divided into three clusters. DEGs from cluster I with downregulated pattern were significantly enriched in cell proliferation processes such as cell cycle, mitotic nuclear division, and DNA replication. DEGs from cluster II with upregulated pattern were significantly enriched in metabolic processes such as glycolysis/gluconeogenesis, insulin signaling pathway, calcium signaling pathway, and biosynthesis of amino acids. DEGs from cluster III, with a pattern that increased from E17 to D1 and then decreased from D1 to D14, mainly contributed to lipid metabolism. Therefore, this study may help us explain the mechanisms underlying the phenotype that myofiber hyperplasia occurs predominantly during embryogenesis and hypertrophy occurs mainly after birth at the transcriptional level. Moreover, lipid metabolism may contribute to the early muscle development and growth. These findings add to our knowledge of muscle development in chickens.
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Affiliation(s)
- Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
- Shandong Provincial Key Laboratory of Poultry Diseases Diagnosis and Immunology, Jinan, China
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Transcriptional insights into key genes and pathways controlling muscle lipid metabolism in broiler chickens. BMC Genomics 2019; 20:863. [PMID: 31729950 PMCID: PMC6858653 DOI: 10.1186/s12864-019-6221-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Background Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological pathways likely contributing to the extreme differences in the TG content of broiler chickens. Results The study included Jingxing-Huang broilers that were significantly different in TG content (5.81 mg/g and 2.26 mg/g, p < 0.01) and deposition of cholesterol also showed the same trend. This RNA sequencing analysis was performed on pectoralis muscle samples from the higher TG content group (HTG) and the lower TG content group (LTG) chickens. A total of 1200 differentially expressed genes (DEGs) were identified between two groups, of which 59 DEGs were related to TG and steroid metabolism. The HTG chickens overexpressed numerous genes related to adipogenesis and lipogenesis in pectoralis muscle tissue, including the key genes ADIPOQ, CD36, FABP4, FABP5, LPL, SCD, PLIN1, CIDEC and PPARG, as well as genes related to steroid biosynthesis (DHCR24, LSS, MSMO1, NSDHL and CH25H). Additionally, key pathways related to lipid storage and metabolism (the steroid biosynthesis and peroxisome proliferator activated receptor (PPAR) signaling pathway) may be the key pathways regulating differential lipid deposition between HTG group and LTG group. Conclusions This study showed that increased TG deposition accompanying an increase in steroid synthesis in pectoralis muscle tissue. Our findings of changes in gene expression of steroid biosynthesis and PPAR signaling pathway in HTG and LTG chickens provide insight into genetic mechanisms involved in different lipid deposition patterns in pectoralis muscle tissue.
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Zhang M, Li F, Ma XF, Li WT, Jiang RR, Han RL, Li GX, Wang YB, Li ZY, Tian YD, Kang XT, Sun GR. Identification of differentially expressed genes and pathways between intramuscular and abdominal fat-derived preadipocyte differentiation of chickens in vitro. BMC Genomics 2019; 20:743. [PMID: 31615399 PMCID: PMC6794883 DOI: 10.1186/s12864-019-6116-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The distribution and deposition of fat tissue in different parts of the body are the key factors affecting the carcass quality and meat flavour of chickens. Intramuscular fat (IMF) content is an important factor associated with meat quality, while abdominal fat (AbF) is regarded as one of the main factors affecting poultry slaughter efficiency. To investigate the differentially expressed genes (DEGs) and molecular regulatory mechanisms related to adipogenic differentiation between IMF- and AbF-derived preadipocytes, we analysed the mRNA expression profiles in preadipocytes (0d, Pre-) and adipocytes (10d, Ad-) from IMF and AbF of Gushi chickens. RESULTS AbF-derived preadipocytes exhibited a higher adipogenic differentiation ability (96.4% + 0.6) than IMF-derived preadipocytes (86.0% + 0.4) (p < 0.01). By Ribo-Zero RNA sequencing, we obtained 4403 (2055 upregulated and 2348 downregulated) and 4693 (2797 upregulated and 1896 downregulated) DEGs between preadipocytes and adipocytes in the IMF and Ad groups, respectively. For IMF-derived preadipocyte differentiation, pathways related to the PPAR signalling pathway, ECM-receptor interaction and focal adhesion pathway were significantly enriched. For AbF-derived preadipocyte differentiation, the steroid biosynthesis pathways, calcium signaling pathway and ECM-receptor interaction pathway were significantly enriched. A large number of DEGs related to lipid metabolism, fatty acid metabolism and preadipocyte differentiation, such as PPARG, ACSBG2, FABP4, FASN, APOA1 and INSIG1, were identified in our study. CONCLUSION This study revealed large transcriptomic differences between IMF- and AbF-derived preadipocyte differentiation. A large number of DEGs and transcription factors that were closely related to fatty acid metabolism, lipid metabolism and preadipocyte differentiation were identified in the present study. Additionally, the microenvironment of IMF- and AbF-derived preadipocyte may play a significant role in adipogenic differentiation. This study provides valuable evidence to understand the molecular mechanisms underlying adipogenesis and fat deposition in chickens.
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Affiliation(s)
- Meng Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.,The First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Xiang-Fei Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Wen-Ting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Rui-Rui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Rui-Li Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Guo-Xi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Yan-Bin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Zi-Yi Li
- The First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Ya-Dong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Xiang-Tao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Gui-Rong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. .,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
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