This study presents genome-wide chromatin state maps for mouse pluripotent and lineage-committed cells using single molecule-based sequencing technology. The researchers profiled histone modifications in mouse embryonic stem cells (ESCs), neural progenitor cells (NPCs), and embryonic fibroblasts (MEFs). They identified distinct chromatin states associated with gene expression, poised genes, and stable repression. Key findings include the role of H3K4me3 and H3K27me3 in distinguishing gene states, H3K36me3 in marking primary transcripts, and H3K9me3 and H4K20me3 in silencing repetitive elements. The study also shows that chromatin state can be read allele-specifically using single nucleotide polymorphisms. The results provide a framework for comprehensive chromatin profiling to characterize diverse mammalian cell populations. The study highlights the importance of chromatin state in cellular identity and lineage commitment, and demonstrates the utility of chromatin state maps for understanding gene regulation and developmental processes. The findings suggest that chromatin state maps can be used to identify novel promoters, primary transcripts, and regulatory elements, and to study the regulation of non-coding RNAs and imprinting. The study also shows that chromatin state maps can be used to analyze allele-specific transcription and imprinting. The results suggest that chromatin state maps can provide a powerful tool for understanding gene regulation and cellular identity in mammals.This study presents genome-wide chromatin state maps for mouse pluripotent and lineage-committed cells using single molecule-based sequencing technology. The researchers profiled histone modifications in mouse embryonic stem cells (ESCs), neural progenitor cells (NPCs), and embryonic fibroblasts (MEFs). They identified distinct chromatin states associated with gene expression, poised genes, and stable repression. Key findings include the role of H3K4me3 and H3K27me3 in distinguishing gene states, H3K36me3 in marking primary transcripts, and H3K9me3 and H4K20me3 in silencing repetitive elements. The study also shows that chromatin state can be read allele-specifically using single nucleotide polymorphisms. The results provide a framework for comprehensive chromatin profiling to characterize diverse mammalian cell populations. The study highlights the importance of chromatin state in cellular identity and lineage commitment, and demonstrates the utility of chromatin state maps for understanding gene regulation and developmental processes. The findings suggest that chromatin state maps can be used to identify novel promoters, primary transcripts, and regulatory elements, and to study the regulation of non-coding RNAs and imprinting. The study also shows that chromatin state maps can be used to analyze allele-specific transcription and imprinting. The results suggest that chromatin state maps can provide a powerful tool for understanding gene regulation and cellular identity in mammals.