Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 7]

In this study, we generated genome-wide data sets for four histone modifications, including H3K9ac, H3K27ac, RNA pol II, H3K9me3, which were collected from MDBK cell line before and after (24h) Butyrate treatment. By combining other types of data sets collected in Rumen Epithelial Primary Cells (REPC) , inclduing four histone codes, CTCF, DNA accessibility, DNA methylation, and RNA-seq, we established and validated 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: The MDBK cell line was purchased from ATCC (ATCC CCL-22; Manassas, VA, USA) and grown in Eagle’s essential medium with 5% fetal bovine serum. For butyrate treatment, 5 mM butyrate was added to the culture medium for 24-h. ChIP-seq of MDBK cells were performed as reported in our earlier publication. In short, DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt single end reads, using an Illumina HiSeq 2500 platform.