Genome-Wide Landscape of Active Enhancers in Sheep Alveolar Macrophages

Lung macrophages provide a first line of defense for the cell-mediated innate immune system against many inhaled pathogens. Annotation of regulatory elements within these cells aids advanced understanding of gene regulation. Acetylation of lysine 27 on histone protein three (H3K27ac) is one of the most dynamic marks, denoting active enhancer regions of the genome. Changes in H3K27ac correspond to changes in gene expression that control cellular differentiation. In this study, alveolar macrophages were harvested from the lungs of a healthy, one-year-old, mixed breed sheep. Chromatin immunoprecipitation with high throughput sequencing (ChIP-seq) was performed for histone modification mark H3K27ac. Approximately 50,000 peaks were identified in the immunoprecipitation data set over control input DNA. Peaks with a false discovery rate of less than 1% included 10,199 peaks with an average enrichment of twenty-fold. This is comparable to published data from humans and other mammalian species for active enhancer marks. Average peak length was 1900 base pairs, which is consistent with expected values of approximately 200-2000 base pairs for mammalian enhancers. However, sequence motif discovery in sheep suggested many are unique when compared with known enhancer motifs in humans, indicative of sequence divergence between species. To our knowledge this is the first report on ChIP-seq for histone marks in sheep immune cells. These data provide a basis for regulatory landscape comparison among sheep cell types and for cross-species comparative regulome analysis in macrophages and immune cells.