STANDARD_NAME MEISSNER_BRAIN_ICP_WITH_H3K4ME3 SYSTEMATIC_NAME M1939 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MEISSNER_BRAIN_ICP_WITH_H3K4ME3 NAMESPACE Mouse_RefSeq DESCRIPTION_BRIEF Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in brain. 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: WHOLE_BRAIN: 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_009577,NM_009898,NM_010226,NM_010244,NM_021529,NM_023179,NM_025473,NM_025533,NM_025837,NM_026127,NM_026677,NM_026942,NM_027328,NM_029044,NM_030716,NM_144786,NM_144891,NM_145703,NM_145704,NM_146007,NM_172484,NM_172858,NM_173746,NM_175542,NM_176834,NM_178069,NM_181419,NM_198647 GENE_SYMBOLS WDR83OS,PAK6,CCDC160,SHANK2,CAPN1,RBM4,RPL19,ZIK1,CORO1A,FOXS1,,PPP2R3C,ATP6V1G2,FAM3A,NOSIP,MPI,C5orf34,RAB13,STOML1,PRPF31,DRC3,KCNIP2,GGT7,GDAP1L1,KCNIP2,KCNIP2,COL6A2,NCKAP5,PAK5,TRIQK,RTTN,RNF208,LSG1,,TBC1D22B FOUNDER_NAMES