ABSTRACT
Development in mammals is accompanied by specific de novo and demethylation events that are thought to stabilize differentiated cell phenotypes. We demonstrate that a large percentage of the tissue-specific 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 first few weeks of life. Using. 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 define the molecular rules of 5-methyl-cytosine regulation as an epigenetic mechanism underlying cellular responses to. changing environment.
Subject(s)
DNA Demethylation , Epigenesis, Genetic/physiology , Gene Expression Regulation, Developmental/physiology , Liver/growth & development , Signal Transduction/physiology , 5-Methylcytosine/metabolism , Animals , Animals, Newborn , Cells, Cultured , DNA-Binding Proteins/genetics , Dioxygenases , Female , Hepatocytes/metabolism , High-Throughput Nucleotide Sequencing , Liver/cytology , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Primary Cell Culture , Proto-Oncogene Proteins/genetics , Sequence Analysis, RNAABSTRACT
There is ample evidence that somatic cell differentiation during development is accompanied by extensive DNA demethylation of specific sites that vary between cell types. Although the mechanism of this process has not yet been elucidated, it is likely to involve the conversion of 5mC to 5hmC by Tet enzymes. We show that a Tet2/Tet3 conditional knockout at early stages of B-cell development largely prevents lineage-specific programmed demethylation events. This lack of demethylation affects the expression of nearby B-cell lineage genes by impairing enhancer activity, thus causing defects in B-cell differentiation and function. Thus, tissue-specific DNA demethylation appears to be necessary for proper somatic cell development in vivo.
Subject(s)
B-Lymphocytes/cytology , B-Lymphocytes/physiology , DNA Methylation/genetics , DNA-Binding Proteins/genetics , Epigenesis, Genetic/genetics , Animals , Cell Differentiation/genetics , Cells, Cultured , Mice , Mice, Inbred C57BL , Organ Specificity/geneticsABSTRACT
DNA methylation patterns are set up in a relatively fixed programmed manner during normal embryonic development and are then stably maintained. Using genome-wide analysis, we discovered a postnatal pathway involving gender-specific demethylation that occurs exclusively in the male liver. This demodification is programmed to take place at tissue-specific enhancer sequences, and our data show that the methylation state at these loci is associated with and appears to play a role in the transcriptional regulation of nearby genes. This process is mediated by the secretion of testosterone at the time of sexual maturity, but the resulting methylation profile is stable and therefore can serve as an epigenetic memory even in the absence of this inducer. These findings add a new dimension to our understanding of the role of DNA methylation in vivo and provide the foundations for deciphering how environment can impact on the epigenetic regulation of genes in general.
