Juliana Afonso, Woo Jun Shim, Tainã Figueiredo Cardoso, Jennifer Jéssica Bruscadin, Andressa Oliveira de Lima, Wellison Jarles da Silva Diniz, Bárbara Silva-Vignato, Ingrid Soares Garcia, Wei Liang Andre Tan, Priscila Silva Neubern de Oliveira, Aline Silva Mello Cesar, Gerson Barreto Mourão, Adhemar Zerlotini, Luiz Lehmann Coutinho, Marina Rufino Salinas Fortes, Luciana Correia de Almeida Regitano
{"title":"内洛雷牛生产、胴体和牛肉品质性状相关的表观遗传调控机制。","authors":"Juliana Afonso, Woo Jun Shim, Tainã Figueiredo Cardoso, Jennifer Jéssica Bruscadin, Andressa Oliveira de Lima, Wellison Jarles da Silva Diniz, Bárbara Silva-Vignato, Ingrid Soares Garcia, Wei Liang Andre Tan, Priscila Silva Neubern de Oliveira, Aline Silva Mello Cesar, Gerson Barreto Mourão, Adhemar Zerlotini, Luiz Lehmann Coutinho, Marina Rufino Salinas Fortes, Luciana Correia de Almeida Regitano","doi":"10.3389/fgene.2025.1593444","DOIUrl":null,"url":null,"abstract":"<p><strong>Introduction: </strong>Understanding regulatory mechanisms like epigenetics can help improve beef production, carcass, and meat quality. Epigenetic states are dynamic and shaped by the environment, but due to limited studies and costly detection methods, alternative approaches are needed.</p><p><strong>Objective: </strong>Our aim was to identify candidate regulators linked to production, carcass and beef quality traits by describing genes putatively regulated by epigenetic mechanisms in the muscle of Nelore cattle.</p><p><strong>Methods: </strong>We <i>in-silico</i> identified discordantly regulated genes (DRGs) with the TRIAGE method and rank product analysis, using gene expression. We investigated the DRGs for being known bovine transcription factors (TFs) or co-factors (TcoFs) and tested the association of SNPs harbouring the DRGs with the traits. Using public muscle ATAC-Seq and ChIP-Seq data, we found that the associated SNPs were harboured in open chromatin sections of the genome and/or on histone modification regions.</p><p><strong>Results: </strong>We identified 51 DRGs across the traits and provided evidence of their regulatory status. 26 DRGs are known bovine TFs. A SNP upstream of the PITX2 DRG was associated with conjugated linoleic acid (CLA), 35 SNPs within or around the BTNL9 DRG were associated with backfat thickness (BFT) and 13 of the DRGs showed a regulatory impact over at least one trait.</p><p><strong>Discussion: </strong>The correlations identified among DRGs, differentially expressed genes and traits showed intricate relationships with various TFs and TcoFs, revealing the putative relationships of these elements with the traits. The <i>LBX1</i> and <i>HOXC10</i> genes are candidates with evidence to be regulators of the traits, while also being subjected to epigenetic regulation.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1593444"},"PeriodicalIF":2.8000,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245772/pdf/","citationCount":"0","resultStr":"{\"title\":\"Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle.\",\"authors\":\"Juliana Afonso, Woo Jun Shim, Tainã Figueiredo Cardoso, Jennifer Jéssica Bruscadin, Andressa Oliveira de Lima, Wellison Jarles da Silva Diniz, Bárbara Silva-Vignato, Ingrid Soares Garcia, Wei Liang Andre Tan, Priscila Silva Neubern de Oliveira, Aline Silva Mello Cesar, Gerson Barreto Mourão, Adhemar Zerlotini, Luiz Lehmann Coutinho, Marina Rufino Salinas Fortes, Luciana Correia de Almeida Regitano\",\"doi\":\"10.3389/fgene.2025.1593444\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Introduction: </strong>Understanding regulatory mechanisms like epigenetics can help improve beef production, carcass, and meat quality. 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Using public muscle ATAC-Seq and ChIP-Seq data, we found that the associated SNPs were harboured in open chromatin sections of the genome and/or on histone modification regions.</p><p><strong>Results: </strong>We identified 51 DRGs across the traits and provided evidence of their regulatory status. 26 DRGs are known bovine TFs. A SNP upstream of the PITX2 DRG was associated with conjugated linoleic acid (CLA), 35 SNPs within or around the BTNL9 DRG were associated with backfat thickness (BFT) and 13 of the DRGs showed a regulatory impact over at least one trait.</p><p><strong>Discussion: </strong>The correlations identified among DRGs, differentially expressed genes and traits showed intricate relationships with various TFs and TcoFs, revealing the putative relationships of these elements with the traits. 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Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle.
Introduction: Understanding regulatory mechanisms like epigenetics can help improve beef production, carcass, and meat quality. Epigenetic states are dynamic and shaped by the environment, but due to limited studies and costly detection methods, alternative approaches are needed.
Objective: Our aim was to identify candidate regulators linked to production, carcass and beef quality traits by describing genes putatively regulated by epigenetic mechanisms in the muscle of Nelore cattle.
Methods: We in-silico identified discordantly regulated genes (DRGs) with the TRIAGE method and rank product analysis, using gene expression. We investigated the DRGs for being known bovine transcription factors (TFs) or co-factors (TcoFs) and tested the association of SNPs harbouring the DRGs with the traits. Using public muscle ATAC-Seq and ChIP-Seq data, we found that the associated SNPs were harboured in open chromatin sections of the genome and/or on histone modification regions.
Results: We identified 51 DRGs across the traits and provided evidence of their regulatory status. 26 DRGs are known bovine TFs. A SNP upstream of the PITX2 DRG was associated with conjugated linoleic acid (CLA), 35 SNPs within or around the BTNL9 DRG were associated with backfat thickness (BFT) and 13 of the DRGs showed a regulatory impact over at least one trait.
Discussion: The correlations identified among DRGs, differentially expressed genes and traits showed intricate relationships with various TFs and TcoFs, revealing the putative relationships of these elements with the traits. The LBX1 and HOXC10 genes are candidates with evidence to be regulators of the traits, while also being subjected to epigenetic regulation.
Frontiers in GeneticsBiochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
5.50
自引率
8.10%
发文量
3491
审稿时长
14 weeks
期刊介绍：
Frontiers in Genetics publishes rigorously peer-reviewed research on genes and genomes relating to all the domains of life, from humans to plants to livestock and other model organisms. Led by an outstanding Editorial Board of the world’s leading experts, this multidisciplinary, open-access journal is at the forefront of communicating cutting-edge research to researchers, academics, clinicians, policy makers and the public.
The study of inheritance and the impact of the genome on various biological processes is well documented. However, the majority of discoveries are still to come. A new era is seeing major developments in the function and variability of the genome, the use of genetic and genomic tools and the analysis of the genetic basis of various biological phenomena.
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