Title:	Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle.
Authors:	AFONSO, J. SHIM, W. J. CARDOSO, T. F. BRUSCADIN, J. J. LIMA, A. O. de DINIZ, W. J. da S. SILVA-VIGNATO, B. GARCIA, I. S. TAN, W. L. A. OLIVEIRA, P. S. N. de CESAR, A. S. M. MOURÃO, G. B. ZERLOTINI NETO, A. COUTINHO, L. L. FORTES, M. R. S. REGITANO, L. C. de A.
Affiliation:	JULIANA AFONSO, THE UNIVERSITY OF QUEENSLAND; WOO JUN SHIM, THE UNIVERSITY OF QUEENSLAND; TAINÃ FIGUEIREDO CARDOSO; JENNIFER JÉSSICA BRUSCADIN, UNIVERSIDADE FEDERAL DE SAO CARLOS; ANDRESSA OLIVEIRA DE LIMA, UNIVERSITY OF WASHINGTON; WELLISON JARLES DA SILVA DINIZ, AUBURN UNIVERSITY; BÁRBARA SILVA-VIGNATO, UNIVERSIDADE DE SÃO PAULO; INGRID SOARES GARCIA, UNIVERSIDADE DE SÃO PAULO; WEI LIANG ANDRE TAN, THE UNIVERSITY OF QUEENSLAND; PRISCILA SILVA NEUBERN DE OLIVEIRA, UNIVERSIDADE FEDERAL DE SAO CARLOS; ALINE SILVA MELLO CESAR, UNIVERSIDADE DE SÃO PAULO; GERSON BARRETO MOURÃO, UNIVERSIDADE DE SÃO PAULO; ADHEMAR ZERLOTINI NETO, CNPTIA; LUIZ LEHMANN COUTINHO, UNIVERSIDADE DE SÃO PAULO; MARINA RUFINO SALINAS FORTES, THE UNIVERSITY OF QUEENSLAND; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE.
Date Issued:	2025
Citation:	Frontiers in Genetics, v. 16, 1593444, 2025.
Description:	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.
Thesagro:	Gado Nelore Carcaça
NAL Thesaurus:	Beef cattle Beef carcasses Beef quality
Keywords:	Regulação epigenética Qualidade de carne bovina Epigenetic regulation
ISSN:	1664-8021
DOI:	https://doi.org/10.3389/fgene.2025.1593444
Notes:	Na publicação: Adhemar Zerlotini.
Type of Material:	Artigo de periódico
Access:	openAccess
Appears in Collections:	Artigo em periódico indexado (CNPTIA)