Expression profiles in the complete absence of DNA methylation [Agilent-028005]

Using all three CpG DNA methyltransferases, Dnmt1, Dnmt3a and Dnmt3b deficient (TKO) mouse ES cells and TKO ntTS cells, we examined three histone modifications H3K4me2, H3K27me3 and H3K9me2, of promoter region in ES, TS and Flk1+ mesodermal cells with WT or TKO background by ChIP-chip analysis. Global profile analysis of gene expression and histone modification showed that the difference of profiles was mainly lineage dependent. Although the effects of DNA methylation loss in three lineages were modest, H3K27me3 is most sensitive to DNA methylation among three modifications. Interestingly, differentially expressed genes between WT and TKO cells were also lineage dependent and small number of genes was overlapped between lineages. Our further analysis showed that the profiles of H3K27me3 modifications were dynamically changed between lineages, especially in TS cells, and the pattern of H3K27me3 modification was defectively established by loss of DNA methylation. Our data suggest that DNA methylation contributes to lineage dependent expression regulation by collaborating with histone modification. Expression profiles in the complete absence of DNA methylation by using Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray. Gene expression was measured in mouse ES cells, Flk+ mesodermal cells and nuclear transferred TS cells with Dnmt1, Dnmt3a and Dnmt3b triple-konockout (TKO) and WT background with duplication, in total 12 samples.