Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 6]

In this study, we generated genome-wide data sets for four histone modifications, including H3K9ac, H3K27ac, RNA pol II, H3K9me3,, which were collected from rumen tissues before and after 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: Rumen tissues were collected before and after 24-h butyrate treatment. 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.

本研究中，我们针对四种组蛋白修饰（包括H3K9ac、H3K27ac、RNA聚合酶II、H3K9me3）生成了全基因组数据集，这些数据集均来源于在丁酸处理前后采集的瘤胃组织。通过整合瘤胃上皮原代细胞（REPC）中收集的其他类型数据集，包括四种组蛋白编码、CTCF、DNA可及性、DNA甲基化和RNA测序数据，我们建立了并验证了首个全局调控元件图谱（15种染色质状态），并定义了其在牛体内的协同活动。我们首次建立了营养元素、染色质状态、基因活性和表型结果之间的相关性。总体设计为：在24小时丁酸处理前后采集瘤胃组织。通过常规ChIP程序回收的DNA使用Promega公司（Madison，WI）的QuantiFluor荧光计进行定量。使用Agilent Bioanalyzer 2100（Agilent；Palo Alto，CA，USA）验证DNA完整性。随后，按照制造商的说明，使用Illumina样本制备试剂盒对DNA进行处理，包括端修复、接头连接和大小选择。最终的DNA文库经过验证，并使用Illumina HiSeq 2500平台进行75-nt单端测序。