The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present wholegenome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissuespecific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development.The accurate spatial and temporal expression of genes is crucial for mammalian embryonic development, and epigenetic regulation is important for controlling the precise tissue-or developmental stage-specific expression patterns of those genes (1-16). Enhancers are one of the most important types of regulatory elements for controlling spatiotemporal gene expression patterns (11,(17)(18)(19)(20)(21)(22)(23). It is well known that distal regulatory elements, such as active enhancers, are normally marked by the combination of H3K27ac and H3K4me1, whereas poised enhancers are marked by only H3K4me1 (24). H3K4me3 normally marks the promoter regions of active/permissive genes, whereas H3K27me3 marks the promoter and gene body regions of repressed genes (25-29). To better understand the regulatory mechanisms during early human embryonic development, it is necessary to analyze the global profiles of these crucial epigenetic markers in the genomes of different human embryonic tissues. However, because of the scarcity of the materials that are available for analysis, a comprehensive chromatin immunoprecipitation (ChIP)-seq analysis of early human embryos has not yet been achieved. We attempted to isolate tissues from three representative organs from the three germ layers, namely the brain, heart, and liver, from human embryos at 12 weeks of gestation, and we systematically analyzed the epigenetic markers H3K27ac, H3K4me1, H3K4me3, and H3K27me3 using a ChIP-seq approach. Moreover, we also analyzed the bivalent H3K4me3/H3K27me3 domains in these three organs via sequential ChIP-seq. As a control, we also downloaded the ChIP-seq data for the corresponding markers in human embryonic stem cells (hESCs) 7 and those for the adult human brain, heart, and liver from the ENCODE database (30, 31). We detected highly reproducible patterns of dynamic epigenetic changes in both the enhancer regions and other functional geno...