Global analysis reveals HDAC1 occupies active and inactive genes and core transcription factors in embryonic stem cells and trophoblast stem cells. Mus musculus

Epigenetic regulation of gene expression is important in maintaining self-renewal of embryonic stem (ES) cells and trophoblast stem (TS) cells. Histone deacetylases (HDACs) negatively control histone acetylation by removing covalent acetylation marks from histone tails. Because histone acetylation is a known mark for active transcription, HDACs presumably associate with inactive genes. Here, we used genome-wide chromatin immunoprecipitation to investigate targets of HDAC1 in ES cells and TS cells. Through evaluation of genes associated with acetylated histone H3 marks, and global expression analysis of Hdac1 knockout ES cells and trichostatin A treated ES cells and TS cells, we found that HDAC1 occupies mainly active genes, including important regulators of ES cell and TS cell self-renewal. By mapping HDAC1 targets on a global scale, our results describe further insight into epigenetic mechanisms of ES cell and TS cell self-renewal. Overall design: RNA was harvested from ES cells and TS cells cultured in the presence of 0 nM, 10 nM, 50 nM, or 100 nM Trichostatin A (TSA) for 24 hours for transcriptome analysis.