Human Gene Set: MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3


Standard name MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3
Systematic name M1941
Brief description Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation at K4 (H3K4me2) and trimethylation at K27 (H3K27me3) in brain.
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
      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: WHOLE_BRAIN: HCP, K4ME3_K27ME3
Related gene sets (show 14 additional gene sets from the source publication)

(show 605 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Jessica Robertson (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)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)

Legacy heatmaps (PNG)
GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 1074 genes
Gene families ? Categorize these 1074 genes by gene family
Show members (show 1164 source identifiers mapped to 1074 genes)
Version history 3.1: First introduced

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