Characterizing cis-regulatory elements associated with mammary gland function

The goal of this study is to improve the quality, efficiency, and sustainability of milk production by improving the understanding of the function of cis-regulatory elements in regulating the bovine mammary gland. To this end, we have characterized the non-lactating and lactating mammary gland transcriptomes by whole transcriptome shotgun sequencing (RNA-seq). We will identify cis-regulatory elements in the non-lactating and lactating bovine mammary gland genome-wide. Finally, we will annotate and characterize mammary gland cis-regulatory elements by computational analysis and identify high-resolution genome-wide in vivo footprints of diverse trans-acting-factors (TF), over-represented TF bindings sites and overlapping SNPs. Overall design: RNA-Seq analysis of 31 samples of mammary epithelial organoids isolated from mammary gland biopsies taken from 16 dairy cows at two time points. 15 samples are derived from biopsies performed at 14 months of age on virgin animals, and 16 samples are derived from biopsies of the same animals at mid-lactation (40-60 days lactation). For one animal, only the lactating sample was suitable for RNA-Seq.