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Feng H, Yousuf S, Liu T, Zhang X, Huang W, Li A, Xie L, Miao X. The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig. Sci Rep 2022; 12:16542. [PMID: 36192451 PMCID: PMC9530237 DOI: 10.1038/s41598-022-21045-2] [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: 05/06/2022] [Accepted: 09/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractcircRNAs, as miRNA sponges, participate in many important biological processes. However, it remains unclear whether circRNAs can regulate lipid metabolism. This study aimed to explore the competing endogenouse RNA (ceRNA) regulatory network that affects the difference between intramuscular fat (IMF) and subcutaneous fat (SCF) deposition, and to screen key circRNAs and their regulatory genes. In this experiment, we identified 265 differentially expressed circRNAs, of which 187 up-regulated circRNA and 78 down-regulated circRNA in IMF. Subsequently, we annotated the function of DEcircRNA's host genes, and found that DEcircRNA's host genes were mainly involved in GO terms (including cellular response to fatty acids, lysophosphatidic acid acyltransferase activity, R-SMAD binding, etc.) and signaling pathways (fatty acid biosynthesis, Citrate cycle, TGF- β Signal pathway) related to adipogenesis, differentiation and lipid metabolism. By constructing a circRNA-miRNA network, we screened out DEcircRNA that can competitively bind to more miRNAs as key circRNAs (circRNA_06424 and circRNA_08840). Through the functional annotation of indirect target genes and protein network analysis, we found that circRNA_06424 affects the expression of PPARD, MMP9, UBA7 and other indirect target genes by competitively binding to miRNAs such as ssc-miR-339-5p, ssc-miR-744 and ssc-miR-328, and participates in PPAR signaling pathway, Wnt signaling pathway, unsaturated fatty acid and other signaling pathways, resulting in the difference of fat deposition between IMF and SCF. This study provide a theoretical basis for further research investigating the differences of lipid metabolism in different adipose tissues, providing potential therapeutic targets for ectopic fat deposition and lipid metabolism diseases.
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Feng H, Liu T, Yousuf S, Zhang X, Huang W, Li A, Xie L, Miao X. Identification of potential miRNA-mRNA regulatory network and the key miRNAs in intramuscular and subcutaneous adipose. Front Vet Sci 2022; 9:976603. [PMID: 36090166 PMCID: PMC9453844 DOI: 10.3389/fvets.2022.976603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Intramuscular fat (IMF) is an important indicator for evaluating meat quality. Breeds with high IMF content are often accompanied by high subcutaneous fat (SCF), severely affecting the meat rate of pigs. Studying the mechanisms of miRNAs related to lipogenesis and lipid metabolism has important implications for pig breeding. We constructed two small RNA libraries from intramuscular and subcutaneous fat to evaluate the patterns of lipogenesis in Laiwu pig, a Chinese breed. A total of 286 differentially expressed miRNAs (DEmiRNAs), including 193 known miRNA and 93 novel miRNAs, were identified from two types of adipose. GO and KEGG enrichment analysis for DEmiRNAs showed that their target genes involved in many adipogenesis and lipid metabolism biological processes and signaling pathways, such as Wnt signaling pathway,MAPK signaling pathway, Hippo signaling pathway, PI3K-Akt signaling pathway, Melanogenesis, Signaling pathways regulating pluripotency of stem cells and so on. Then, we constructed a miRNA-mRNA interaction network to find out which miRNAs were the key miRNAs of regulation in Wnt signaling pathway. In this pathway, miR-331-3p, miR-339-5p, miR-874 and novel346_mature target PPARD, WNT10B, RSPO3, WNT2B. This study provides a theoretical basis for further understanding the post-transcriptional regulation mechanism of meat quality formation and predicting and treating diseases caused by ectopic fat.
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Zhang P, Li Q, Wu Y, Zhang Y, Zhang B, Zhang H. Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs. Sci Rep 2022; 12:2844. [PMID: 35181733 PMCID: PMC8857214 DOI: 10.1038/s41598-022-06868-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.
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Affiliation(s)
- Pan Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yijing Wu
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
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Le TH, Christensen OF, Nielsen B, Sahana G. Genome-wide association study for conformation traits in three Danish pig breeds. Genet Sel Evol 2017; 49:12. [PMID: 28118822 PMCID: PMC5259967 DOI: 10.1186/s12711-017-0289-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 01/12/2017] [Indexed: 02/07/2023] Open
Abstract
Background Selection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses. Methods Data on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses. Estimated effects of single nucleotide polymorphisms (SNPs) from single-trait association analyses were combined in two meta-analyses: (1) a within-breed meta-analysis for multiple traits to examine if there are pleiotropic genetic variants within a breed; and (2) an across-breed meta-analysis for a single trait to examine if the same quantitative trait loci (QTL) segregate across breeds. SNP annotation was implemented through Sus scrofa Build 10.2 on Ensembl to search for candidate genes. Results Among the 14, 12 and 13 QTL that were detected in the single-trait association analyses for the three breeds, the most significant SNPs explained 2, 2.3 and 11.4% of genetic variance for back quality in Landrace, overall conformation in Yorkshire and back quality in Duroc, respectively. Several candidate genes for these QTL were also identified, i.e. LRPPRC, WRAP73, VRTN and PPARD likely control conformation traits through the regulation of bone and muscle development, and IGF2BP2, GH1, CCND2 and MSH2 can have an influence through growth-related processes. Meta-analyses not only confirmed many significant SNPs from single-trait analyses with higher significance levels, but also detected several additional associated SNPs and suggested QTL with possible pleiotropic effects. Conclusions Our results imply that conformation traits are complex and may be partly controlled by genes that are involved in bone and skeleton development, muscle and fat metabolism, and growth processes. A reliable list of QTL and candidate genes was provided that can be used in fine-mapping and marker assisted selection to improve conformation traits in pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0289-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thu H Le
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark. .,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Ole F Christensen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Bjarne Nielsen
- SEGES Pig Research Centre, Axeltorv, Copenhagen, Denmark
| | - Goutam Sahana
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
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Meyer SU, Krebs S, Thirion C, Blum H, Krause S, Pfaffl MW. Tumor Necrosis Factor Alpha and Insulin-Like Growth Factor 1 Induced Modifications of the Gene Expression Kinetics of Differentiating Skeletal Muscle Cells. PLoS One 2015; 10:e0139520. [PMID: 26447881 PMCID: PMC4598026 DOI: 10.1371/journal.pone.0139520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/13/2015] [Indexed: 12/19/2022] Open
Abstract
Introduction TNF-α levels are increased during muscle wasting and chronic muscle degeneration and regeneration processes, which are characteristic for primary muscle disorders. Pathologically increased TNF-α levels have a negative effect on muscle cell differentiation efficiency, while IGF1 can have a positive effect; therefore, we intended to elucidate the impact of TNF-α and IGF1 on gene expression during the early stages of skeletal muscle cell differentiation. Methodology/Principal Findings This study presents gene expression data of the murine skeletal muscle cells PMI28 during myogenic differentiation or differentiation with TNF-α or IGF1 exposure at 0 h, 4 h, 12 h, 24 h, and 72 h after induction. Our study detected significant coregulation of gene sets involved in myoblast differentiation or in the response to TNF-α. Gene expression data revealed a time- and treatment-dependent regulation of signaling pathways, which are prominent in myogenic differentiation. We identified enrichment of pathways, which have not been specifically linked to myoblast differentiation such as doublecortin-like kinase pathway associations as well as enrichment of specific semaphorin isoforms. Moreover to the best of our knowledge, this is the first description of a specific inverse regulation of the following genes in myoblast differentiation and response to TNF-α: Aknad1, Cmbl, Sepp1, Ndst4, Tecrl, Unc13c, Spats2l, Lix1, Csdc2, Cpa1, Parm1, Serpinb2, Aspn, Fibin, Slc40a1, Nrk, and Mybpc1. We identified a gene subset (Nfkbia, Nfkb2, Mmp9, Mef2c, Gpx, and Pgam2), which is robustly regulated by TNF-α across independent myogenic differentiation studies. Conclusions This is the largest dataset revealing the impact of TNF-α or IGF1 treatment on gene expression kinetics of early in vitro skeletal myoblast differentiation. We identified novel mRNAs, which have not yet been associated with skeletal muscle differentiation or response to TNF-α. Results of this study may facilitate the understanding of transcriptomic networks underlying inhibited muscle differentiation in inflammatory diseases.
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Affiliation(s)
- Swanhild U Meyer
- Physiology Weihenstephan, ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Freising, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, University of Munich, Ludwig-Maximilians-Universität München, München, Germany
| | - Sabine Krause
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Michael W Pfaffl
- Physiology Weihenstephan, ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Freising, Germany
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The function of porcine PPARγ and dietary fish oil effect on the expression of lipid and glucose metabolism related genes. J Nutr Biochem 2011; 22:179-86. [DOI: 10.1016/j.jnutbio.2010.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 01/09/2010] [Accepted: 01/14/2010] [Indexed: 12/27/2022]
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Nutritional intervention during gestation alters growth, body composition and gene expression patterns in skeletal muscle of pig offspring. Animal 2011; 5:1195-206. [DOI: 10.1017/s1751731111000176] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Yu YH, Wang PH, Cheng WTK, Mersmann HJ, Wu SC, Ding ST. Porcine peroxisome proliferator-activated receptor delta mediates the lipolytic effects of dietary fish oil to reduce body fat deposition. J Anim Sci 2010; 88:2009-18. [PMID: 20190170 DOI: 10.2527/jas.2009-2597] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Peroxisome proliferator-activated receptor delta promotes fatty acid catabolism and energy expenditure in skeletal muscle and adipose tissues. A ligand for PPARdelta is required to activate PPARdelta function. Polyunsaturated fatty acids are potential ligands for PPARdelta activation. The current experiment was designed to determine the potential for PUFA, particularly from dietary fish oil, to activate porcine PPARdelta in vivo. Transgenic mice were generated to overexpress porcine PPARdelta in the adipose tissue. Mice were fed a high-saturated fat (13% beef tallow), or high-unsaturated fat (13% fish oil) diet, or a diet containing 4 mg/kg of a PPARdelta ligand (L165041) for 4 mo. Compared with beef tallow feeding, fish oil feeding reduced fat mass and decreased (P < 0.05) plasma triacylglycerol and FFA concentrations in the transgenic mice. Adipose tissue expression of genes involved in adipogenesis (i.e., lipoprotein lipase and adipocyte fatty acid-binding protein) was decreased in transgenic mice fed fish oil or the PPARdelta ligand. In the same mice, expression of the lipolytic gene, hormone-sensitive lipase was increased (P < 0.05). Fish oil feeding also stimulated expression of genes participating in fatty acid oxidation in the liver of transgenic mice compared with wild-type mice. Overall, these results indicate that PUFA may serve as natural and effective regulators of lipid catabolism in vivo and many of these effects may be generated from activation of PPARdelta.
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Affiliation(s)
- Y H Yu
- Department of Animal Science and Technology/Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
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Rhoads RP, Fernyhough ME, Liu X, McFarland DC, Velleman SG, Hausman GJ, Dodson MV. Extrinsic regulation of domestic animal-derived myogenic satellite cells II. Domest Anim Endocrinol 2009; 36:111-26. [PMID: 19261429 DOI: 10.1016/j.domaniend.2008.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 12/12/2022]
Abstract
The existence of myogenic satellite cells was reported some 47 years ago, and, since that time, satellite cell research has flourished. So much new information is generated (daily) on these cells that it can be difficult for individuals to keep abreast of important issues related to their activation and proliferation, the modulation of the activity of other cell types, the differentiation of the cells to facilitate normal skeletal muscle growth and development, or to the repair of damaged myofibers. The intent of this review is to summarize new information about the extrinsic regulation of myogenic satellite cells and to provide specific mechanisms involved in altering satellite cell physiology. Where possible, examples from agriculturally important animals are used for illustrative purposes.
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Affiliation(s)
- R P Rhoads
- Department of Animal Sciences, University of Arizona, Tucson, AZ 85719, USA
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