Epigenomic Landscape of Human Fetal Brain, Heart, and Liver

• Published in: The Journal of biological chemistry Vol. 291; no. 9; pp. 4386 - 4398
• Main Authors: Yan, Liying, Guo, Hongshan, Hu, Boqiang, Li, Rong, Yong, Jun, Zhao, Yangyu, Zhi, Xu, Fan, Xiaoying, Guo, Fan, Wang, Xiaoye, Wang, Wei, Wei, Yuan, Wang, Yan, Wen, Lu, Qiao, Jie, Tang, Fuchou
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 26.02.2016; American Society for Biochemistry and Molecular Biology
• Subjects: Aborted Fetus - metabolism; Biomarkers - metabolism; Brain - embryology; Brain - metabolism; China; Chromatin - chemistry; Chromatin - metabolism; Databases, Nucleic Acid; development; Developmental Biology; Epigenesis, Genetic; epigenetics; Gene Expression Regulation, Developmental; Gene Ontology; gene regulation; Genomic Library; genomics; Heart - embryology; high throughput screening; High-Throughput Nucleotide Sequencing; Histones - genetics; Histones - metabolism; Humans; Liver - embryology; Liver - metabolism; Lysine - metabolism; Methylation; Myocardium - metabolism; Organ Specificity; Protein Processing, Post-Translational; Sequence Analysis, DNA; Species Specificity; China; genomics; development; gene regulation; high throughput screening; epigenetics
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1074/jbc.M115.672931

The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome 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 tissue-specific 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.