Predicting Chromatin State in Bovine Pluripotent Cells

Despite cattle’s similarity to human preimplantation development, the open chromatin landscape structure that underlies bovine pluripotency has remained relatively uncharacterized. The initially repressive chromatin landscape present in differentiated gametes must undergo extensive remodeling after fertilization to become open and permissive of transcription – a state characteristic of pluripotency. To determine nucleosome-free regions (NFR) that may be key to pluripotency, two pluripotent cell types – in vitro produced blastocysts (BL) and embryonic stem cells (ESC) – were subjected to ATAC-seq (Assay for Transposase-Accessible Chromatin). Pluripotent-specific NFR were enriched for motifs associated with pluripotency, such as SOX2, OCT4, NANOG, GATA2 and GATA4, and frequently occurred in promoters. Genes with pluripotent-specific NFR within their promoters were more likely to be expressed, and were highly associated with gene expression and mRNA processing. Through integration of chromatin accessibility, gene expression, and histone modification data, chromatin state was predicted genome-wide. These results provide insight into the putative regulatory roles of and how they may be implicated in the pluripotent state both in embryos and in culture.