Epigenetic Regulation in Bos indicus Rumen Tissue: Influences on Host Gene Expression and Interactions with the Microbiome

• Grant number: 24/17528-2
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: August 01, 2025
• End date: July 31, 2028
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Luciana Correia de Almeida Regitano
• Grantee: Jennifer Jessica Bruscadin
• Host Institution: Embrapa Pecuária Sudeste. Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA). Ministério da Agricultura, Pecuária e Abastecimento (Brasil). São Carlos , SP, Brazil
• Associated research grant: 19/04089-2 - The Nelore hologenome: implications in beef quality and feed efficiency, AP.ESCIENCE.TEM

Abstract

Epigenetics affects gene transcription without altering the nucleotide sequence and can interact with the composition of the ruminant microbiota, which has functions related to digestive system homeostasis and complex phenotypes. This study will investigate the interaction between epigenomes, transcriptomes, and metagenomes obtained from the same rumen samples of Nelore cattle (Bos indicus) using methods for predicting functional regions and multi-omic integration, contributing to the understanding of the microbiota's influence on epigenetic regulation, as well as the consequences of the later on gene expression and microbiota composition. The experimental population consists of 52 rumen tissue samples from Nelore cattle for which multi-omics data are available, including transcriptome and metagenome data. For eight of these samples, epigenome data from ChIP-seq are available, containing peaks of four histone modifications and the transcription factor CTCF, as well as ATAC-seq data, identifying chromatin regions accessible for transcription factor binding. Functional regions will be investigated through the prediction of chromatin states, epigenetic and allele-specific regulatory mechanisms, expanding knowledge on gene and taxa regulation relevant to animal production and the identification of functional variants. This work is innovative because no study has so far consistently addressed epigenetic regulation in ruminal tissue with such a complete multi-omics dataset as the one presented here. In addition to having the largest sample population with epigenetic data, appropriate methods will be applied for the available sample sizes. These results will complement the objectives of the thematic project "The Nelore Hologenome: implications for meat quality and feed efficiency" (Process: 2019/04089-2), connecting to the results of other related projects, in the quest to better understand the regulation dynamics of complex phenotypes. (AU)