Identification of Lactation-Related cis-Regulatory Regions in the Bovine Genome

Assay for transposase-accessible chromatin (ATAC)-seq allows the unbiased in vivo mapping of cis-regulatory elements. RNA sequencing (RNA-Seq) enables the analysis of the genes that are expressed to produce milk. Combining these approaches allows us to investigate the regulatory regions that orchestrate the transcriptional changes that mark the transition to the lactating state. In the current study, we isolated mammary epithelial organoids from biopsies taken from the glands of the same 15 dairy cows before their first pregnancy (approximately 14 months of age) and at peak lactation (40–60 days lactation) for RNA-seq and ATACseq. Over 8,000 genes were differentially expressed between virgin and lactation with 111 genes that were isoform-specific. We identified a single significant instance of transcription start site (TSS) switching, though many more genes were found to be using more than one TSS in both the virgin and lactating gland. ATAC-Seq was optimized and libraries were generated for virgin and peak lactation samples. We are now integrating genomic, epigenetic, and transcriptomic data to identify lactation-related cis-regulatory regions in the bovine genome.