Gene Set: MIKKELSEN_ES_HCP_WITH_H3K27ME3

Standard name MIKKELSEN_ES_HCP_WITH_H3K27ME3
Systematic name M2000
Brief description Genes with high-CpG-density promoters (HCP) bearing histone H3 K27 trimethylation mark (H327me3) in embryonic stem cells (ES).
Full description or abstract We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 17603471   Authors: Mikkelsen TS,Ku M,Jaffe DB,Issac B,Lieberman E,Giannoukos G,Alvarez P,Brockman W,Kim TK,Koche RP,Lee W,Mendenhall E,O'Donovan A,Presser A,Russ C,Xie X,Meissner A,Wernig M,Jaenisch R,Nusbaum C,Lander ES,Bernstein BE
Exact source Table 4S: Class=HCP & ESC state=K27
Related gene sets (show 15 additional gene sets from the source publication)

(show 583 gene sets from the same authors)
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Organism Mus musculus
Contributed by Arthur Liberzon (Broad Institute)
Source platform MOUSE_GENE_SYMBOL
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.1: First introduced

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