Functional annotation of regulatory elements in cattle genome reveals the roles of extracellular interaction and dynamic change of chromatin states in rumen development during weaning

We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning. The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined through genome-wide profiling of four histone modifications, CTCF-binding, DNA accessibility, DNA methylation, and transcriptome in rumen epithelial tissues. Each chromatin state presented specific enrichment for sequence ontology, methylation, trait-associated variants, transcription, gene expression-associated variants, selection signatures, and evolutionarily conserved elements. During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states and occurred in tandem with significant variations in gene expression and DNA methylation, significantly associated with stature, production, and reproduction economic traits. By comparing with in vitro cultured epithelial cells and in vivo rumen tissues, we showed the commonness and uniqueness of these results, especially the roles of cell interactions and mitochondrial activities in tissue development. •We profiled landscapes of bovine regulatory elements and explored dynamic changes of chromatin states in rumen development during weaning.•The regulatory elements (15 chromatin states) and their coordinated activities in cattle were defined•Each chromatin state presented specific enrichment for functional regulatory elements.•During weaning, weak enhancers and flanking active transcriptional start sites (TSS) were the most dynamic chromatin states.•With in vivo rumen tissues, we showed the roles of cell interactions and mitochondrial activities in tissue development.