Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle
Beef cattle raised under grass-fed and grain-fed have many differences, including metabolic efficiency and meat quality. To investigate these two regimens' intrinsic influence on beef cattle, we used high-throughput sequencing and metabolomics analyses to explore differentially expressed genes...
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.579393/full |
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| author | Cunling Jia Cunling Jia Ying Bai Jianan Liu Wentao Cai Lei Liu Lei Liu Yanghua He Jiuzhou Song |
| author_facet | Cunling Jia Cunling Jia Ying Bai Jianan Liu Wentao Cai Lei Liu Lei Liu Yanghua He Jiuzhou Song |
| author_sort | Cunling Jia |
| collection | DOAJ |
| description | Beef cattle raised under grass-fed and grain-fed have many differences, including metabolic efficiency and meat quality. To investigate these two regimens' intrinsic influence on beef cattle, we used high-throughput sequencing and metabolomics analyses to explore differentially expressed genes (DEGs) and metabolimic networks in the liver. A total of 200 DEGs, 76 differentially expressed miRNAs (DEmiRNAs), and two differentially expressed lncRNAs (DElncRNAs) were detected between regimen groups. Metabolic processes and pathways enriched functional genes including target genes of miRNAs and lncRNAs. We found that many genes were involved in energy, retinol and cholesterol metabolism, and bile acid synthesis. Combined with metabolites such as low glucose concentration, high cholesterol concentration, and increased primary bile acid concentration, these genes were mainly responsible for lowering intramuscular fat, low cholesterol, and yellow meat in grass-fed cattle. Additionally, we identified two lncRNAs and eight DEGs as potential competing endogenous RNAs (ceRNAs) to bind miRNAs by the interaction network analysis. These results revealed that the effects of two feeding regimens on beef cattle were mainly induced by gene expression changes in metabolic pathways mediated via lncRNAs, miRNAs, and ceRNAs, and contents of metabolites in the liver. It may provide a clue on feeding regimens inducing the metabolic regulations. |
| first_indexed | 2024-12-17T08:45:36Z |
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| id | doaj.art-e8f0947aa1ac42399c5e0efb9478a54b |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-17T08:45:36Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-e8f0947aa1ac42399c5e0efb9478a54b2022-12-21T21:56:12ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-03-011210.3389/fgene.2021.579393579393Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef CattleCunling Jia0Cunling Jia1Ying Bai2Jianan Liu3Wentao Cai4Lei Liu5Lei Liu6Yanghua He7Jiuzhou Song8College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaDepartment of Animal & Avian Science, University of Maryland, College Park, MD, United StatesDepartment of Animal & Avian Science, University of Maryland, College Park, MD, United StatesDepartment of Animal & Avian Science, University of Maryland, College Park, MD, United StatesDepartment of Animal & Avian Science, University of Maryland, College Park, MD, United StatesDepartment of Animal & Avian Science, University of Maryland, College Park, MD, United StatesResearch Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Science, Shenzhen, ChinaDepartment of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Manoa, HI, United StatesDepartment of Animal & Avian Science, University of Maryland, College Park, MD, United StatesBeef cattle raised under grass-fed and grain-fed have many differences, including metabolic efficiency and meat quality. To investigate these two regimens' intrinsic influence on beef cattle, we used high-throughput sequencing and metabolomics analyses to explore differentially expressed genes (DEGs) and metabolimic networks in the liver. A total of 200 DEGs, 76 differentially expressed miRNAs (DEmiRNAs), and two differentially expressed lncRNAs (DElncRNAs) were detected between regimen groups. Metabolic processes and pathways enriched functional genes including target genes of miRNAs and lncRNAs. We found that many genes were involved in energy, retinol and cholesterol metabolism, and bile acid synthesis. Combined with metabolites such as low glucose concentration, high cholesterol concentration, and increased primary bile acid concentration, these genes were mainly responsible for lowering intramuscular fat, low cholesterol, and yellow meat in grass-fed cattle. Additionally, we identified two lncRNAs and eight DEGs as potential competing endogenous RNAs (ceRNAs) to bind miRNAs by the interaction network analysis. These results revealed that the effects of two feeding regimens on beef cattle were mainly induced by gene expression changes in metabolic pathways mediated via lncRNAs, miRNAs, and ceRNAs, and contents of metabolites in the liver. It may provide a clue on feeding regimens inducing the metabolic regulations.https://www.frontiersin.org/articles/10.3389/fgene.2021.579393/fulllncRNAsmiRNAsceRNAsbeef cattlefeeding regimensmetabolic regulations |
| spellingShingle | Cunling Jia Cunling Jia Ying Bai Jianan Liu Wentao Cai Lei Liu Lei Liu Yanghua He Jiuzhou Song Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle Frontiers in Genetics lncRNAs miRNAs ceRNAs beef cattle feeding regimens metabolic regulations |
| title | Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle |
| title_full | Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle |
| title_fullStr | Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle |
| title_full_unstemmed | Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle |
| title_short | Metabolic Regulations by lncRNA, miRNA, and ceRNA Under Grass-Fed and Grain-Fed Regimens in Angus Beef Cattle |
| title_sort | metabolic regulations by lncrna mirna and cerna under grass fed and grain fed regimens in angus beef cattle |
| topic | lncRNAs miRNAs ceRNAs beef cattle feeding regimens metabolic regulations |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.579393/full |
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