Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls
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 proces...
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MDPI AG
2020-06-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/6/700 |
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| author | Bilal Ahmad Mir Henry Reyer Katrin Komolka Siriluck Ponsuksili Christa Kühn Steffen Maak |
| author_facet | Bilal Ahmad Mir Henry Reyer Katrin Komolka Siriluck Ponsuksili Christa Kühn Steffen Maak |
| author_sort | Bilal Ahmad Mir |
| collection | DOAJ |
| description | 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 F<sub>2</sub>-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 <i>p</i>-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. |
| first_indexed | 2024-03-10T18:53:47Z |
| format | Article |
| id | doaj.art-e3e690e14b694acc919b1cc587315601 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T18:53:47Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-e3e690e14b694acc919b1cc5873156012023-11-20T04:57:31ZengMDPI AGGenes2073-44252020-06-0111670010.3390/genes11060700Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred BullsBilal Ahmad Mir0Henry Reyer1Katrin Komolka2Siriluck Ponsuksili3Christa Kühn4Steffen Maak5Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, GermanyInstitute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, GermanyInstitute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, GermanyInstitute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, GermanyInstitute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, GermanyInstitute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, GermanyIntramuscular 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 F<sub>2</sub>-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 <i>p</i>-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.https://www.mdpi.com/2073-4425/11/6/700intramuscular fatadipogenesislipid metabolismmiRNAmicroarraybioinformatics |
| spellingShingle | Bilal Ahmad Mir Henry Reyer Katrin Komolka Siriluck Ponsuksili Christa Kühn Steffen Maak Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls Genes intramuscular fat adipogenesis lipid metabolism miRNA microarray bioinformatics |
| title | Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls |
| title_full | Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls |
| title_fullStr | Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls |
| title_full_unstemmed | Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls |
| title_short | Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F<sub>2</sub>-Crossbred Bulls |
| title_sort | differentially expressed mirna gene targets related to intramuscular fat in musculus longissimus dorsi of charolais holstein f sub 2 sub crossbred bulls |
| topic | intramuscular fat adipogenesis lipid metabolism miRNA microarray bioinformatics |
| url | https://www.mdpi.com/2073-4425/11/6/700 |
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