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Li R, Zhu R, Yang X, Feng Y, He Q, Wang H, Liu Q, Shi D, Huang J. The role of lncFABP4 in modulating adipogenic differentiation in buffalo intramuscular preadipocytes. Anim Sci J 2024; 95:e13951. [PMID: 38703069 DOI: 10.1111/asj.13951] [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: 08/17/2023] [Revised: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 05/06/2024]
Abstract
Intramuscular fat (IMF) is a crucial determinant of meat quality and is influenced by various regulatory factors. Despite the growing recognition of the important role of long noncoding RNAs (lncRNAs) in IMF deposition, the mechanisms underlying buffalo IMF deposition remain poorly understood. In this study, we identified and characterized a lncRNA, lncFABP4, which is transcribed from the antisense strand of fatty acid-binding protein 4 (FABP4). lncFABP4 inhibited cell proliferation in buffalo intramuscular preadipocytes. Moreover, lncFABP4 significantly increased intramuscular preadipocyte differentiation, as indicated by an increase in the expression of the adipogenic markers peroxisome proliferator-activated receptor gamma (PPARG), CCAAT enhancer binding protein alpha (C/EBPα), and FABP4. Mechanistically, lncFABP4 was found to have the potential to regulate downstream gene expression by participating in protein-protein interaction pathways. These findings contribute to further understanding of the intricate mechanisms through which lncRNAs modulate intramuscular adipogenesis in buffaloes.
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Affiliation(s)
- Ruirui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Xintong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Ye Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Qin He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Haopeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
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Abstract
Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.
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Affiliation(s)
- Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Shuang Liu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Honghong Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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Huang J, Feng X, Zhu R, Guo D, Wei Y, Cao X, Ma Y, Shi D. Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo. BMC Genomics 2020; 21:710. [PMID: 33045988 PMCID: PMC7552535 DOI: 10.1186/s12864-020-07120-w] [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: 03/31/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition. RESULTS To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the longissimus dorsi muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 (PCK1) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the PCK1 promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of PCK1 in buffalo promoter is higher than that in cattle. CONCLUSIONS These results indicate the important role of PCK1 in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive PCK1 expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China. .,College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.,School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
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Mir BA, Reyer H, Komolka K, Ponsuksili S, Kühn C, Maak S. Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F 2-Crossbred Bulls. Genes (Basel) 2020; 11:genes11060700. [PMID: 32630492 PMCID: PMC7348786 DOI: 10.3390/genes11060700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) is a meat quality indicator associated with taste and juiciness. IMF deposition, influenced by genetic and non-genetic factors, occurs through a transcriptionally coordinated process of adipogenesis. MicroRNAs (miRNAs) are transcriptional regulators of vital biological processes, including lipid metabolism and adipogenesis. However, in bovines, limited data on miRNA profiling and association with divergent intramuscular fat content, regulated exclusively by genetic parameters, have been reported. Here, a microarray experiment was performed to identify and characterize the miRNA expression pattern in the Musculus longissimus dorsi of F2-cross (Charolais × German Holstein) bulls with high and low IMF. A total of 38 differentially expressed miRNAs (DE miRNAs), including 33 upregulated and 5 downregulated (corrected p-value ≤ 0.05, FC ≥ ±1.2), were reported. Among DE miRNAs, the upregulated miRNAs miR-105a/b, miR-695, miR-1193, miR-1284, miR-1287-5p, miR-3128, miR-3178, miR-3910, miR-4443, miR-4445 and miR-4745, and the downregulated miRNAs miR-877-5p, miR-4487 and miR-4706 were identified as novel fat deposition regulators. DE miRNAs were further analyzed, along with previously identified differentially expressed genes (DEGs) from the same samples and predicted target genes, using multiple bioinformatic approaches, including target prediction tools and co-expression networks, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We identified DE miRNAs and their gene targets associated with bovine intramuscular adipogenesis, and we provide a basis for further functional investigations.
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Affiliation(s)
- Bilal Ahmad Mir
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (K.K.); (S.M.)
- Correspondence: ; Tel.: +49-38208-68885
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (H.R.); (S.P.); (C.K.)
| | - Katrin Komolka
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (K.K.); (S.M.)
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (H.R.); (S.P.); (C.K.)
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (H.R.); (S.P.); (C.K.)
| | - Steffen Maak
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (K.K.); (S.M.)
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Huang J, Wang S, Feng X, Liu X, Zhao J, Zheng Q, Wei X, Ma Y. miRNA transcriptome comparison between muscle and adipose tissues indicates potential miRNAs associated with intramuscular fat in Chinese swamp buffalo. Genome 2019; 62:729-738. [PMID: 31398299 DOI: 10.1139/gen-2018-0178] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The amount of intramuscular fat (IMF) affects the tenderness and juiciness of beef and is an important indicator of beef quality. A few miRNAs involved in IMF deposition have been identified in other livestock. However, in the buffalo, the association between miRNA and IMF has not been reported and the miRNA expression profile remains poorly understood. In this study, small RNA sequencing was performed to characterize the miRNA expression pattern in muscle and adipose tissues using the Illumina platform. A total of 108 differentially expressed (DE) miRNAs were identified, including 98 known miRNAs and 10 novel miRNAs. A qRT-PCR experiment confirmed the quality of the DE analysis. Eight DE miRNAs showed high expression in adipose tissue and a considerable expression level in muscle tissue. Functional enrichment indicated that bta-miR-148a, bta-miR-143, bta-miR-10b, bta-let-7i, bta-let-7f, bta-let-7b, bta-miR-30a-5p, and bta-miR-100 were significantly associated with adipogenesis, suggesting these as candidate regulators for IMF deposition in buffalo. However, further functional validation is required. This is the first characterization of the miRNA expression profile in the muscle and adipose tissues of buffalo. These results provide information for the identification of miRNAs with potential effects on IMF deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Shuzhe Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Xiaoyan Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Jinhui Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Qiuzhi Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, 464000, China.,School of Agriculture, Ningxia University, Yinchuan, Ningxia, 750021, China
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Martínez del Pino L, Arana A, Alfonso L, Mendizábal JA, Soret B. Adiposity and adipogenic gene expression in four different muscles in beef cattle. PLoS One 2017; 12:e0179604. [PMID: 28665940 PMCID: PMC5493301 DOI: 10.1371/journal.pone.0179604] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/01/2017] [Indexed: 02/06/2023] Open
Abstract
Anatomical site and divergent functionalities of muscles can be related to differences in IMF content, metabolism and adipogenic gene expression. Then, potential differences in different muscles in beef cattle were studied. As a second objective, the main sources of experimental variability associated to RT-qPCR results were analyzed following a nested design in order to implement appropriate experimental designs minimizing gene expression variability. To perform the study Longissimus thoracis (LT), Semitendinosus (SM), Masseter (MS), Sternomandibularis (ST) and subcutaneous adipose tissue (SAT) samples of Pirenaica young bulls (n = 4) were collected for IMF, collagen and protein quantification, analysis of adipocyte size distribution and gene expression (PPARG, CEBPA, FAPB4 and WNT10B). A greater IMF content was observed in MS and SM muscles, which had a bimodal adipocyte size distribution while it was unimodal in the muscles LT and ST. This suggest that the different IMF accretion in the muscles studied might be related to different rates of hyperplasia and hypertrophy and that IMF might develop later in LT and ST muscles. The former differences were not mirrored by the expression of the genes analyzed, which might be related to the different contribution of mature and non-mature adipocytes to the total gene expression. When comparing IMF and SAT gene expression, late and early developing tissues respectively, expression of PPARG, CEBPA and FABP4 was higher in the SAT, in agreement with bigger cell size and numbers. The variability study indicates that the analytical factors that add higher variability to the gene expression are the sampling and RT and therefore, it would be appropriate to include those replicates in the design of future experiments. Based on the results, the use of MS and SM muscles could allow less expensive experimental designs and bigger sample size that could permit the detection of lower relevant differences in gene expression.
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Affiliation(s)
- Lara Martínez del Pino
- Escuela Superior de Ingenieros Agrónomos, Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
| | - Ana Arana
- Escuela Superior de Ingenieros Agrónomos, Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
| | - Leopoldo Alfonso
- Escuela Superior de Ingenieros Agrónomos, Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
| | - José Antonio Mendizábal
- Escuela Superior de Ingenieros Agrónomos, Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
| | - Beatriz Soret
- Escuela Superior de Ingenieros Agrónomos, Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
- * E-mail:
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