Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 4]

In this study, we generated CTCF and four histone modifications, including H3K27ac, H3K27m3, H3K4m1, H3K4m3, which were collected from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing RNA polymerase II, DNA accessibility, and RNA-seq, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes. Overall design: Rumen primary epithelial cells were isolated from a two-week-old Holstein bull calf fed with milk replacer only. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24 hrs. CTCF-seq and ChIP-Seq of H3K27ac, H3K27m3, H3K4m1, H3K4m3, of rumen primary epithelial cells (RPEC) were performed at Active Motif according to proprietary methods. For ChIP-seq, CTCF-seq, the 75-nt single end reads were generated using NextSeq 500 (Active Motif, Inc. Carlsbad, CA, USA).