Program in Bioinformatics and Integrative Biology; Graduate School of Biomedical Sciences
Cell Biology | Developmental Biology | Genomics | Integrative Biology
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.
Epigenetic memory, Genome informatics, Epigenomics, Gene regulation
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DOI of Published Version
van der Velde A, Fan K, Tsuji J, Moore JE, Purcaro MJ, Pratt HE, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Commun Biol. 2021 Feb 22;4(1):239. doi: 10.1038/s42003-021-01756-4. PMID: 33619351; PMCID: PMC7900196. Link to article on publisher's site
van der Velde A, Fan K, Tsuji J, Moore JE, Purcaro MJ, Pratt HE, Weng Z. (2021). Annotation of chromatin states in 66 complete mouse epigenomes during development. Open Access Publications by UMMS Authors. https://doi.org/10.1038/s42003-021-01756-4. Retrieved from https://escholarship.umassmed.edu/oapubs/4591
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This work is licensed under a Creative Commons Attribution 4.0 License.