Systematic name M13611
Brief description Unmethylated germline-specific genes with low-CpG-density promoters (LCP) 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 gene sets
      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: LCP, 5mC (log2) in fibroblasts < 0
Related gene sets (show 10 additional gene sets from the source publication)

(show 4 gene sets from the same authors)
External links  
Organism Homo sapiens
Contributed by Arthur Liberzon (Broad Institute)
Source platform HUMAN_GENE_SYMBOL
Dataset references  
Download gene set format: grp | text | gmt | gmx | xml
Compute overlaps (show collections to investigate for overlap with this gene set)
Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 10 genes
Gene families Categorize these 10 genes by gene family
Show members (show 10 members mapped to 10 genes)
Version history 3.0: First introduced

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