Human Gene Set: WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN


Standard name WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN
Systematic name M16646
Brief description Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts.
Full description or abstract To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic and germline cells. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in male gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates. In contrast, strong CpG island promoters are mostly unmethylated, even when inactive. Weak CpG island promoters are distinct, as they are preferential targets for de novo methylation in somatic cells. Notably, most germline-specific genes are methylated in somatic cells, suggesting additional functional selection. These results show that promoter sequence and gene function are major predictors of promoter methylation states. Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 17334365   Authors: Weber M,Hellmann I,Stadler MB,Ramos L,Pääbo S,Rebhan M,Schübeler D
Exact source Table 1S: HCP, 5mC (log2) in fibroblasts > 0
Related gene sets (show 10 additional gene sets from the source publication)

(show 4 gene sets from any of these authors)
External links
Filtered by similarity ?
Source species Homo sapiens
Contributed by Jessica Robertson (MSigDB Team)
Source platform or
identifier namespace		 HUMAN_GENE_SYMBOL
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 43 genes
Gene families ? Categorize these 43 genes by gene family
Show members (show 43 source identifiers mapped to 43 genes)
Version history 3.0: First introduced

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