Epigenetic regulation of gene expression is important in maintaining 
self-renewal of embryonic stem (ES) 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 and TS cells. Through evaluation of genes associated with 
acetylated histone H3 marks, and global expression analysis of Hdac1 knockout ES 
and trichostatin A-treated ES and TS cells, we found that HDAC1 occupies mainly 
active genes, including important regulators of ES and TS cells self-renewal. We 
also observed occupancy of methyl-CpG binding domain protein 3 (MBD3), a subunit 
of the nucleosome remodeling and histone deacetylation (NuRD) complex, at a 
subset of HDAC1-occupied sequences in ES cells, including the pluripotency 
regulators Oct4, Nanog and Kfl4. By mapping HDAC1 targets on a global scale, our 
results describe further insight into epigenetic mechanisms of ES and TS cells 
self-renewal.