STANDARD_NAME	MEISSNER_ES_ICP_WITH_H3K4ME3
SYSTEMATIC_NAME	MM815
COLLECTION	M2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/mouse/geneset/MEISSNER_ES_ICP_WITH_H3K4ME3
NAMESPACE	Mouse_RefSeq
DESCRIPTION_BRIEF	Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in ES cells (embryonic stem).
DESCRIPTION_FULL	DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.
PMID	18600261
GEOID	GSE11172
AUTHORS	Meissner A,Mikkelsen TS,Gu H,Wernig M,Hanna J,Sivachenko A,Zhang X,Bernstein BE,Nusbaum C,Jaffe DB,Gnirke A,Jaenisch R,Lander ES
CONTRIBUTOR	Jessica Robertson
CONTRIBUTOR_ORG	MSigDB Team
EXACT_SOURCE	Table 2S: ES: ICP, K4me3
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	NM_001001493,NM_001033254,NM_001034059,NM_001081370,NM_007600,NM_009032,NM_009078,NM_009317,NM_009577,NM_010102,NM_010244,NM_011905,NM_021529,NM_023179,NM_025473,NM_025533,NM_025837,NM_026127,NM_026677,NM_026942,NM_027328,NM_027419,NM_028877,NM_029044,NM_030716,NM_144848,NM_144891,NM_145703,NM_145704,NM_146007,NM_172484,NM_173746,NM_175542,NM_176834,NM_178069,NM_181419,NM_198647
GENE_SYMBOLS	Wdr83os,Pak6,Ccdc160,Shank2,Capn1,Rbm4,Rpl19,Tal2,Zik1,S1pr4,Fv1,Tlr2,Ppp2r3c,Atp6v1g2,Fam3a,Nosip,Mpi,4833420G17Rik,Rab13,Stoml1,Prpf31,2810408A11Rik,Palm3,Drc3,Kcnip2,Eppk1,Gdap1l1,Kcnip2,Kcnip2,Col6a2,Nckap5,Triqk,Rttn,Rnf208,Lsg1,Zfp599,Tbc1d22b
FOUNDER_NAMES