Gene Set: MEISSNER_NPC_ICP_WITH_H3K4ME3

Standard name MEISSNER_NPC_ICP_WITH_H3K4ME3
Systematic name M1934
Brief description Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural precursor cells (NPC).
Full description or abstract 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.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 18600261   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
Exact source Table 2S: NPC(P18): ICP, K4me3
Related gene sets (show 14 additional gene sets from the source publication)

(show 601 gene sets from the same authors)
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Organism Mus musculus
Contributed by Jessica Robertson (Broad Institute)
Source platform SEQ_ACCESSION
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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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