Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle
Abstract This study aimed to identify differentially expressed (DE) long non-coding RNAs (lncRNAs) in muscle tissue of Nellore cattle clustered by their fatty acid profile. Longissimus thoracis muscle samples from 48 young bulls were used to quantify fatty acid (FA) (myristic, palmitic, stearic, ole...
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Nature Portfolio
2025-07-01
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| Online Access: | https://doi.org/10.1038/s41598-025-11179-4 |
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| author | Bruna Maria Salatta Maria Malane Magalhães Muniz Larissa Fernanda Simielli Fonseca Lucio Flavio Macedo Mota Caio de Souza Teixeira Gabriela Bonfá Frezarim Marta Serna-García Danielly Beraldo dos Santos Silva Angélica Simone Cravo Pereira Fernando Baldi Lucia Galvão de Albuquerque |
| author_facet | Bruna Maria Salatta Maria Malane Magalhães Muniz Larissa Fernanda Simielli Fonseca Lucio Flavio Macedo Mota Caio de Souza Teixeira Gabriela Bonfá Frezarim Marta Serna-García Danielly Beraldo dos Santos Silva Angélica Simone Cravo Pereira Fernando Baldi Lucia Galvão de Albuquerque |
| author_sort | Bruna Maria Salatta |
| collection | DOAJ |
| description | Abstract This study aimed to identify differentially expressed (DE) long non-coding RNAs (lncRNAs) in muscle tissue of Nellore cattle clustered by their fatty acid profile. Longissimus thoracis muscle samples from 48 young bulls were used to quantify fatty acid (FA) (myristic, palmitic, stearic, oleic, linoleic, conjugated linoleic (CLA), α-linolenic and the groups of saturated fatty acids (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), ω3, ω6, PUFA/SFA ratio and ω6/ω3) and to generate RNA-Sequencing data for transcriptomic analyses. The K-means analysis was used to classify the 48 animals into three clusters based on their FA patterns. The C1 had significantly (p ≤ 0.05) higher PUFA, ω3, ω6, linoleic and α-linolenic content. The proportion of SFA, myristic, palmitic and stearic were significantly (p ≤ 0.05) higher in C3, while C2 presented an intermediate profile. DE analyses were performed on three different comparisons, C1 vs. C2, C1 vs. C3 and C2 vs. C3, and 22, 28 and 22 DE lncRNAs (fold change > | 2 |, p-value < 0.01 and false discovery rate (FDR) < 0.05) were found, respectively. For three comparisons, the novel DE transcripts, lncRNA_15786.3, lncRNA_13894.1 and lincRNA_17393.3 interacted with CCN1, BNIP3, and CNOT2 genes, respectively, and appeared to contribute to a PUFA-enriched fatty acid profile. These genes are responsible for regulating the lipogenic genes, lipid metabolism, immune response and lipid synthesis. Meanwhile, the intergenic DE lncRNAs (lincRNA_18394.1, lincRNA_2526.3 and lincRNA_17681.1) were associated with the genes DDX1, EIF4E and APOL3, and appeared to contribute to a SFA-enriched fatty acid profile. The gene DDX1 was enriched by GO terms related to RNA splicing (GO:0008380), while the other genes (e.g., EIF4E and APOL3) were enriched to GO terms related to lipid transport (GO:0006869), localization (GO:0010876) and to cellular response to lipid (GO:0071396). These findings offer new insights into the biological mechanisms underlying the gene regulation of FA composition in beef and may provide a valuable foundation for further investigations regarding the interactions between lncRNAs and mRNAs, as well as their potential impact on meat quality. |
| format | Article |
| id | doaj-art-109f68fccad4484c82f11fb01af028ab |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-109f68fccad4484c82f11fb01af028ab2025-08-20T04:01:51ZengNature PortfolioScientific Reports2045-23222025-07-0115112210.1038/s41598-025-11179-4Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattleBruna Maria Salatta0Maria Malane Magalhães Muniz1Larissa Fernanda Simielli Fonseca2Lucio Flavio Macedo Mota3Caio de Souza Teixeira4Gabriela Bonfá Frezarim5Marta Serna-García6Danielly Beraldo dos Santos Silva7Angélica Simone Cravo Pereira8Fernando Baldi9Lucia Galvão de Albuquerque10Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of GuelphAnimal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Nutrition and Animal Production Department, Faculty of Veterinary Medicine and Animal Science, University of São PauloAnimal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp)Abstract This study aimed to identify differentially expressed (DE) long non-coding RNAs (lncRNAs) in muscle tissue of Nellore cattle clustered by their fatty acid profile. Longissimus thoracis muscle samples from 48 young bulls were used to quantify fatty acid (FA) (myristic, palmitic, stearic, oleic, linoleic, conjugated linoleic (CLA), α-linolenic and the groups of saturated fatty acids (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), ω3, ω6, PUFA/SFA ratio and ω6/ω3) and to generate RNA-Sequencing data for transcriptomic analyses. The K-means analysis was used to classify the 48 animals into three clusters based on their FA patterns. The C1 had significantly (p ≤ 0.05) higher PUFA, ω3, ω6, linoleic and α-linolenic content. The proportion of SFA, myristic, palmitic and stearic were significantly (p ≤ 0.05) higher in C3, while C2 presented an intermediate profile. DE analyses were performed on three different comparisons, C1 vs. C2, C1 vs. C3 and C2 vs. C3, and 22, 28 and 22 DE lncRNAs (fold change > | 2 |, p-value < 0.01 and false discovery rate (FDR) < 0.05) were found, respectively. For three comparisons, the novel DE transcripts, lncRNA_15786.3, lncRNA_13894.1 and lincRNA_17393.3 interacted with CCN1, BNIP3, and CNOT2 genes, respectively, and appeared to contribute to a PUFA-enriched fatty acid profile. These genes are responsible for regulating the lipogenic genes, lipid metabolism, immune response and lipid synthesis. Meanwhile, the intergenic DE lncRNAs (lincRNA_18394.1, lincRNA_2526.3 and lincRNA_17681.1) were associated with the genes DDX1, EIF4E and APOL3, and appeared to contribute to a SFA-enriched fatty acid profile. The gene DDX1 was enriched by GO terms related to RNA splicing (GO:0008380), while the other genes (e.g., EIF4E and APOL3) were enriched to GO terms related to lipid transport (GO:0006869), localization (GO:0010876) and to cellular response to lipid (GO:0071396). These findings offer new insights into the biological mechanisms underlying the gene regulation of FA composition in beef and may provide a valuable foundation for further investigations regarding the interactions between lncRNAs and mRNAs, as well as their potential impact on meat quality.https://doi.org/10.1038/s41598-025-11179-4Genic lncRNAslincRNANellore cattleRNA-Seq |
| spellingShingle | Bruna Maria Salatta Maria Malane Magalhães Muniz Larissa Fernanda Simielli Fonseca Lucio Flavio Macedo Mota Caio de Souza Teixeira Gabriela Bonfá Frezarim Marta Serna-García Danielly Beraldo dos Santos Silva Angélica Simone Cravo Pereira Fernando Baldi Lucia Galvão de Albuquerque Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle Scientific Reports Genic lncRNAs lincRNA Nellore cattle RNA-Seq |
| title | Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle |
| title_full | Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle |
| title_fullStr | Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle |
| title_full_unstemmed | Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle |
| title_short | Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle |
| title_sort | skeletal muscle lncrna profile associated with fatty acids in nellore beef cattle |
| topic | Genic lncRNAs lincRNA Nellore cattle RNA-Seq |
| url | https://doi.org/10.1038/s41598-025-11179-4 |
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