The Dynamics of Chromatin Accessibility Prompted by Butyrate-Induced Chromatin Modification in Bovine Cells

Abstract

Butyrate is produced by microbe fermentation in the rumen, and its supplementation results in rumen development. Butyrate-induced experiments are valuable in studying nutrient metabolism, cell growth, and functional genomics. This study aimed to characterize accessible chromatin regions and the dynamics of genomic accessibility prompted by butyrate-induced histone modifications in bovine cells. An average of 117,569 accessible chromatin regions were identified for all samples, and 21,347 differentially accessible regions (DARs) for butyrate. Most of the DARs were in distal intergenic regions, introns, and promoters. Gene ontology enrichment resulted in important terms related to the digestive system, regulation of epithelial cells, and cell adhesion. Ingenuity Pathway Analysis (IPA) identified critical networks (e.g., digestive system development, cell morphology and assembly, and cell cycle); canonical pathways (e.g., TGFβ, Integrin-linked kinase, and epithelial adherens junction); and upstream regulators (e.g., TGFβ1, FOS, JUNB, ATF3, and KLFs). Co-expression analysis further showcased the TGFβ and Integrin-linked kinase (ILK)-signaling pathways, which play roles in rumen development through cellular adhesions. This study is the first to provide a genome-wide characterization of differential, open chromatin regions for bovine cells by butyrate-induced treatment. These results provide valuable information for future studies of the butyrate functions in cattle gastrointestinal tract development.