Mouse Gene Set: MEISSNER_NPC_HCP_WITH_H3K4ME2

For the Human gene set with the same name, see MEISSNER_NPC_HCP_WITH_H3K4ME2

Standard name MEISSNER_NPC_HCP_WITH_H3K4ME2
Systematic name MM830
Brief description Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) 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 M2: Curated
      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): HCP, K4me2
Related gene sets (show 13 additional gene sets from the source publication)

(show 41 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Arthur Liberzon (MSigDB Team)
Source platform or
identifier namespace		 MOUSE_SEQ_ACCESSION
Dataset references (show 1 datasets)
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
Mouse Transcriptomic BodyMap compendium

Legacy heatmaps (PNG)
Mouse Transcriptomic BodyMap compendium
Advanced query Further investigate these 496 genes
Show members (show 541 source identifiers mapped to 496 genes)
Version history 2022.1.Mm: First Introduced.

See MSigDB license terms here. Please note that certain gene sets have special access terms.