its role in

Development in mammals is accompanied by speci fi c de novo and demethylation events that are thought to stabilize differentiated cell phenotypes. We demonstrate that a large percentage of the tissue-speci fi c methylation pattern is generated postnatally. Demethylation in the liver is observed in thousands of enhancer-like sequences associated with genes that undergo activation during the fi rst few weeks of life. Using a conditional gene ablation strategy we show that the removal of these methyl groups is stable and necessary for assuring proper hepatocyte gene expression and function through its effect on chromatin accessibility. These postnatal changes in methylation come about through exposure to hormone signaling. These results de fi ne the molecular rules of 5-methyl-cytosine regulation as an epigenetic mechanism underlying cellular responses to a changing environment. each one of them contained on average six different samples, we could repeat this process numerous times. In the case of hepatocytes, the original number of hepatocyte-speci fi c unmethylated regions was ~9000, and analysis of 10,000 permutations yielded at most fi ve DMRs. The reason for this very low number is that when comparing mixed tissues to other tissues with our very stringent parameters, it yields almost no DMRs, demonstrating the purity of our DMRS. The p value was calculated to be smaller than 10 − 4 since for 10,000 permutations almost no DMRs were found. DMRs were also validated by the examination of methylation status on new RRBS and WGBS samples that did not participate in the original analysis. In addition, comparison using methylKit in R with similar cutoff criteria detected 4790 DMRs, of which 93% overlapped with the 9291 DMRs generated by our algorithm ( p value <10 − 100 as determined by the χ 2 test of homogeneity). These average of Our studies also us to look at the overall effects of preventing demethylation. example, identi fi ed a total of about 870 genes that are expressed at lower levels in the DKO as compared to WT 20-week hepatocytes and many of these ( n are signi cantly upregulated postnatally. We also detected 790 genes that are actually upregulated in the knockout as compared to WT. These changes may result from indirect effects downstream of the primary methyl-dependent genes or from activities of the TET proteins not related to DNA methylation 52 . Alternately, they may come about as a compensation response to changes in physiology resulting from the DKO. Expression in non-hepatocyte derived from published