G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription

Abstract

Methylation of DNA and lysine 9 of histone H3 (H3K9) are well‐conserved epigenetic marks for transcriptional silencing. Although H3K9 methylation directs DNA methylation in filamentous fungi and plants, this pathway has not been corroborated in mammals. G9a and GLP/Eu‐HMTase1 are two‐related mammalian lysine methyltransferases and a G9a/GLP heteromeric complex regulates H3K9 methylation of euchromatin. To elucidate the function of G9a/GLP‐mediated H3K9 methylation in the regulation of DNA methylation and transcriptional silencing, we characterized ES cells expressing catalytically inactive mutants of G9a and/or GLP. Interestingly, in ES cells expressing a G9a‐mutant/GLP complex that does not rescue global H3K9 methylation, G9a/GLP‐target genes remain silent. The CpG sites of the promoter regions of these genes were hypermethylated in such mutant ES cells, but hypomethylated in G9a‐ or GLP ‐KO ES cells. Treatment with a DNA methyltransferase inhibitor reactivates these G9a/GLP‐target genes in ES cells expressing catalytically inactive G9a/GLP proteins, but not the wild‐type proteins. This is the first clear evidence that G9a/GLP suppresses transcription by independently inducing both H3K9 and DNA methylation.