Human Gene Set: WEBER_METHYLATED_ICP_IN_FIBROBLAST


Standard name WEBER_METHYLATED_ICP_IN_FIBROBLAST
Systematic name M731
Brief description Germline-specific genes with intermediate-CpG-density promoters (ICP) that are methylated 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: ICP, 5mC (log2) in fibroblasts > 0
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Source species Homo sapiens
Contributed by Arthur Liberzon (MSigDB Team)
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identifier namespace		 HUMAN_GENE_SYMBOL
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Version history 3.0: First introduced

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