Transcriptional regulation by epigenetic mechanisms

Restricted until 18 June 2009.Transcriptional regulation can be controlled by epigenetic mechanisms including DNA methylation, histone modifications and nucleosome occupancy. We first mapped histone H3 acetylation and H3-K4 methylation patterns globally across the human genome using our novel genome scanning method called ChAP and showed that they are located preferentially to the transcriptional start sites in the human genome. The strong concordance of these modifications at the 5' regions of genes indicate that these modifications may serve as critical signals for defining the start of the transcribed domain. We then examined these epigenetic parameters in detail using the bidirectional CpG island promoter, MLH1 gene as an example. MLH1, which has two transcriptional start sites and the other gene EPM2AIP1, are coordinately expressed in cell lines with low promoter methylation and both are silenced together in cancer cell lines with promoter hypermethylation, suggesting the promoter acts as a unit. In addition to DNA methylation, silencing of the three transcription start sites in the bidirectional MLH1 promoter in cancer cells also involves distinct changes in nucleosomal occupancy. Three nucleosomes, almost completely absent from the start sites in normal cells, are present on the methylated and silenced promoter, suggesting that epigenetic silencing may be accomplished by the stable placement of nucleosomes into previously vacant positions. Indeed, activation of the promoter by demethylation using 5-aza-2'deoxycytidine involves nucleosome eviction