Afonso Juliana, Jun Shim Woo, Figueiredo Cardoso Tainã, Bruscadin Jennifer Jéssica, Oliveira de Lima Andressa, Jarles da Silva Diniz Wellison, Silva-Vignato Bárbara, Soares Garcia Ingrid, Liang Andre Tan Wei, Silva Neubern de Oliveira Priscila, Silva Mello Cesar Aline, Barreto Mourão Gerson, Zerlotini Adhemar, Lehmann Coutinho Luiz, Rufino Salinas Fortes Marina, Correia de Almeida Regitano Luciana
Animal Biotechnology Group, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
Front Genet. 2025 Jun 27;16:1593444. doi: 10.3389/fgene.2025.1593444. eCollection 2025.
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.
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.
We 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.
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.
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 and genes are candidates with evidence to be regulators of the traits, while also being subjected to epigenetic regulation.
了解表观遗传学等调控机制有助于提高牛肉产量、胴体品质和肉质。表观遗传状态是动态的，受环境影响，但由于研究有限且检测方法成本高昂，需要其他替代方法。
我们的目标是通过描述在Nellore牛肌肉中可能受表观遗传机制调控的基因，来识别与生产、胴体和牛肉品质性状相关的候选调控因子。
我们使用TRIAGE方法和秩乘积分析，通过基因表达来识别差异调控基因（DRGs）。我们研究这些DRGs是否为已知的牛转录因子（TFs）或辅助因子（TcoFs），并测试携带DRGs的单核苷酸多态性（SNPs）与这些性状的关联。利用公开的肌肉ATAC-Seq和ChIP-Seq数据，我们发现相关的SNPs存在于基因组的开放染色质区域和/或组蛋白修饰区域。
我们在这些性状中识别出51个DRGs，并提供了它们调控状态的证据。26个DRGs是已知的牛TFs。PITX2 DRG上游的一个SNP与共轭亚油酸（CLA）相关，BTNL9 DRG内部或周围的35个SNPs与背膘厚度（BFT）相关，并且13个DRGs对至少一个性状显示出调控作用。
在DRGs、差异表达基因和性状之间确定的相关性显示出与各种TFs和TcoFs的复杂关系，揭示了这些元件与性状之间的假定关系。 和 基因是有证据表明是这些性状调控因子的候选基因，同时也受到表观遗传调控。
