STANDARD_NAME	MIKKELSEN_NPC_ICP_WITH_H3K27ME3
SYSTEMATIC_NAME	M2011
COLLECTION	C2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MIKKELSEN_NPC_ICP_WITH_H3K27ME3
NAMESPACE	MOUSE_GENE_SYMBOL
DESCRIPTION_BRIEF	Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC).
DESCRIPTION_FULL	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.
PMID	17603471
GEOID	GSE12241
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
CONTRIBUTOR	Arthur Liberzon
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Table 4S: Class=ICP & NPC state=K27
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	Ccdc108,Fxyd7,H2-T3,Hoxb13,Islr2,Lin28b,Matn1,Mlph,Pou2af1,Pvalb,Rbm35a,Rgs8,Ttll6
GENE_SYMBOLS	CFAP65,FXYD7,,HOXB13,ISLR2,LIN28B,MATN1,MLPH,POU2AF1,PVALB,ESRP1,RGS8,TTLL6
FOUNDER_NAMES