The morphologically and functionally distinct cell types of a multicellular organism are maintained by their unique epigenomes and gene expression programs. Phase III of the ENCODE Project profiled 66 mouse epigenomes across twelve tissues at daily intervals from embryonic day 11.5 to birth. Applying the ChromHMM algorithm to these epigenomes, we annotated eighteen chromatin states with characteristics of promoters, enhancers, transcribed regions, repressed regions, and quiescent regions. Our integrative analyses delineate the tissue specificity and developmental trajectory of the loci in these chromatin states. Approximately 0.3% of each epigenome is assigned to a bivalent chromatin state, which harbors both active marks and the repressive mark H3K27me3. Highly evolutionarily conserved, these loci are enriched in silencers bound by polycomb repressive complex proteins, and the transcription start sites of their silenced target genes. This collection of chromatin state assignments provides a useful resource for studying mammalian development.

多细胞生物的形态和功能不同的细胞类型由其独特的表观基因组和基因表达程序维持。ENCODE 项目的第三阶段从胚胎第 11.5 天到出生每天分析 12 个组织中的 66 个小鼠表观基因组。将 ChromHMM 算法应用于这些表观基因组，我们注释了 18 个具有启动子、增强子、转录区域、抑制区域和静止区域特征的染色质状态。我们的综合分析描述了这些染色质状态下基因座的组织特异性和发育轨迹。每个表观基因组的大约 0.3% 被分配到二价染色质状态，其中包含活性标记和抑制标记 H3K27me3。在进化上高度保守，这些位点富含由多梳抑制复合蛋白结合的消音器，以及它们沉默的靶基因的转录起始位点。这组染色质状态分配为研究哺乳动物发育提供了有用的资源。