STANDARD_NAME WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN SYSTEMATIC_NAME M16646 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN NAMESPACE HUMAN_GENE_SYMBOL DESCRIPTION_BRIEF Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts. DESCRIPTION_FULL 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. PMID 17334365 GEOID GSE6715 AUTHORS Weber M,Hellmann I,Stadler MB,Ramos L,Pääbo S,Rebhan M,Schübeler D CONTRIBUTOR Jessica Robertson CONTRIBUTOR_ORG MSigDB Team EXACT_SOURCE Table 1S: HCP, 5mC (log2) in fibroblasts > 0 FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS ACRBP,ADAM30,ALF,AURKC,BOLL,BRDT,C1orf14,CABYR,CATSPER2,CKLFSF2,DAZL,DKKL1,FTMT,GAPDS,HNRNPG-T,HRLP5,HSPB9,INSL6,LPIN1,MORC,MOV10L1,NYD-SP20,ODF2,PAPOLB,POTE14,POTE15,REC8L1,RPL10L,SOX30,SPACA1,SPO11,SSTK,STK31,SYCP1,SYCP2,TCP11,TPTE,TPX1,TRPM4,TSP50,TULP2,ZPBP,ZPBP2 GENE_SYMBOLS ACRBP,ADAM30,GTF2A1L,AURKC,BOLL,BRDT,SHCBP1L,CABYR,CATSPER2,CMTM2,DAZL,DKKL1,FTMT,GAPDHS,RBMXL2,PLAAT5,HSPB9,INSL6,LPIN1,MORC1,MOV10L1,SPATA22,ODF2,PAPOLB,POTEG,POTEB,REC8,RPL10L,SOX30,SPACA1,SPO11,TSSK6,STK31,SYCP1,SYCP2,TCP11,TPTE,CRISP2,TRPM4,PRSS50,TULP2,ZPBP,ZPBP2 FOUNDER_NAMES