Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle
Epigenetic repression has been linked to the regulation of different cell states. In this study, we focus on the influence of this repression, mainly by H3K27me3, over gene expression in muscle cells, which may affect mineral content, a phenotype that is relevant to muscle function and beef quality....
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | Biochemistry and Biophysics Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405580823000018 |
| _version_ | 1811167222380363776 |
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| author | Juliana Afonso Woo Jun Shim Mikael Boden Marina Rufino Salinas Fortes Wellison Jarles da Silva Diniz Andressa Oliveira de Lima Marina Ibelli Pereira Rocha Tainã Figueiredo Cardoso Jennifer Jessica Bruscadin Caio Fernando Gromboni Ana Rita Araujo Nogueira Gerson Barreto Mourão Adhemar Zerlotini Luiz Lehmann Coutinho Luciana Correia de Almeida Regitano |
| author_facet | Juliana Afonso Woo Jun Shim Mikael Boden Marina Rufino Salinas Fortes Wellison Jarles da Silva Diniz Andressa Oliveira de Lima Marina Ibelli Pereira Rocha Tainã Figueiredo Cardoso Jennifer Jessica Bruscadin Caio Fernando Gromboni Ana Rita Araujo Nogueira Gerson Barreto Mourão Adhemar Zerlotini Luiz Lehmann Coutinho Luciana Correia de Almeida Regitano |
| author_sort | Juliana Afonso |
| collection | DOAJ |
| description | Epigenetic repression has been linked to the regulation of different cell states. In this study, we focus on the influence of this repression, mainly by H3K27me3, over gene expression in muscle cells, which may affect mineral content, a phenotype that is relevant to muscle function and beef quality. Based on the inverse relationship between H3K27me3 and gene expression (i.e., epigenetic repression) and on contrasting sample groups, we computationally predicted regulatory genes that affect muscle mineral content. To this end, we applied the TRIAGE predictive method followed by a rank product analysis. This methodology can predict regulatory genes that might be affected by repressive epigenetic regulation related to mineral concentration. Annotation of orthologous genes, between human and bovine, enabled our investigation of gene expression in the Longissimus thoracis muscle of Bos indicus cattle. The animals under study had a contrasting mineral content in their muscle cells. We identified candidate regulatory genes influenced by repressive epigenetic mechanisms, linking histone modification to mineral content in beef samples. The discovered candidate genes take part in multiple biological pathways, i.e., impulse transmission, cell signalling, immunological, and developmental pathways. Some of these genes were previously associated with mineral content or regulatory mechanisms. Our findings indicate that epigenetic repression can partially explain the gene expression profiles observed in muscle samples with contrasting mineral content through the candidate regulators here identified. |
| first_indexed | 2024-04-10T16:06:46Z |
| format | Article |
| id | doaj.art-24455101b3f54cbe9de541eed20822e7 |
| institution | Directory Open Access Journal |
| issn | 2405-5808 |
| language | English |
| last_indexed | 2024-04-10T16:06:46Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biochemistry and Biophysics Reports |
| spelling | doaj.art-24455101b3f54cbe9de541eed20822e72023-02-10T04:22:48ZengElsevierBiochemistry and Biophysics Reports2405-58082023-03-0133101420Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattleJuliana Afonso0Woo Jun Shim1Mikael Boden2Marina Rufino Salinas Fortes3Wellison Jarles da Silva Diniz4Andressa Oliveira de Lima5Marina Ibelli Pereira Rocha6Tainã Figueiredo Cardoso7Jennifer Jessica Bruscadin8Caio Fernando Gromboni9Ana Rita Araujo Nogueira10Gerson Barreto Mourão11Adhemar Zerlotini12Luiz Lehmann Coutinho13Luciana Correia de Almeida Regitano14Embrapa Pecuária Sudeste, São Carlos, São Paulo, BrazilSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, AustraliaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, AustraliaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, AustraliaDepartment of Animal Sciences, Auburn University, Auburn, AL, USADivision of Medical Genetics, Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, WA, USAPost-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, BrazilEmbrapa Pecuária Sudeste, São Carlos, São Paulo, BrazilPost-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, BrazilBahia Federal Institute of Education, Science and Technology, Ilhéus, BrazilEmbrapa Pecuária Sudeste, São Carlos, São Paulo, BrazilDepartment of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, BrazilBioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, BrazilDepartment of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, BrazilEmbrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil; Corresponding author.Epigenetic repression has been linked to the regulation of different cell states. In this study, we focus on the influence of this repression, mainly by H3K27me3, over gene expression in muscle cells, which may affect mineral content, a phenotype that is relevant to muscle function and beef quality. Based on the inverse relationship between H3K27me3 and gene expression (i.e., epigenetic repression) and on contrasting sample groups, we computationally predicted regulatory genes that affect muscle mineral content. To this end, we applied the TRIAGE predictive method followed by a rank product analysis. This methodology can predict regulatory genes that might be affected by repressive epigenetic regulation related to mineral concentration. Annotation of orthologous genes, between human and bovine, enabled our investigation of gene expression in the Longissimus thoracis muscle of Bos indicus cattle. The animals under study had a contrasting mineral content in their muscle cells. We identified candidate regulatory genes influenced by repressive epigenetic mechanisms, linking histone modification to mineral content in beef samples. The discovered candidate genes take part in multiple biological pathways, i.e., impulse transmission, cell signalling, immunological, and developmental pathways. Some of these genes were previously associated with mineral content or regulatory mechanisms. Our findings indicate that epigenetic repression can partially explain the gene expression profiles observed in muscle samples with contrasting mineral content through the candidate regulators here identified.http://www.sciencedirect.com/science/article/pii/S2405580823000018Bos indicusH3K27me3Epigenetic regulationGene repressionMinerals |
| spellingShingle | Juliana Afonso Woo Jun Shim Mikael Boden Marina Rufino Salinas Fortes Wellison Jarles da Silva Diniz Andressa Oliveira de Lima Marina Ibelli Pereira Rocha Tainã Figueiredo Cardoso Jennifer Jessica Bruscadin Caio Fernando Gromboni Ana Rita Araujo Nogueira Gerson Barreto Mourão Adhemar Zerlotini Luiz Lehmann Coutinho Luciana Correia de Almeida Regitano Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle Biochemistry and Biophysics Reports Bos indicus H3K27me3 Epigenetic regulation Gene repression Minerals |
| title | Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle |
| title_full | Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle |
| title_fullStr | Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle |
| title_full_unstemmed | Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle |
| title_short | Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle |
| title_sort | repressive epigenetic mechanisms such as the h3k27me3 histone modification were predicted to affect muscle gene expression and its mineral content in nelore cattle |
| topic | Bos indicus H3K27me3 Epigenetic regulation Gene repression Minerals |
| url | http://www.sciencedirect.com/science/article/pii/S2405580823000018 |
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