"Deciphering the Epigenetic Code: Molecular Profiling of Histone Post-translational Modifications using FT-ICR Mass Spectrometry"
Regulation of gene expression during development and differentiation of multicellular organisms depends in large parts on transcription complexes and their interaction with chromatin. Modifications of DNA, histone post-translational modifications, histone variants and small nuclear RNAs (SnRNAs) or RNA interference (RNAi), are hypothesized to contribute to epigenetic memory of transcriptional states. These modifications or "marks" promote cellular specificity by imposing a unique and heritable pattern on the progeny of differentiating cells. Remarkably, alterations in these "marks" have been found in nearly every cancer type studied. For example, promoter CpG methylation-mediated silencing of tumor suppressor genes has been associated with many types of cancer. Likewise, histone deacetylase inhibitors are now in Phase I and II clinical trials; and chromatin modifying enzymes are found over expressed, mutated and rearranged in cancer cells.
Histone proteins are key components of chromatin and are potentially important carriers of epigenetic information. Recently, new insights have been gained into how single histone post translational modifications, affect chromatin structure. However, to fully decipher the information capacity of histones, a better understanding of how specific combinations of histone post- translational modifications are generated and how the modification of one residue can affect another. For example, some modifications allow binding of specific proteins whereas other block specific interactions; however, it still not known how each individual modification is read and if certain sets of modification always occur together.
The overall aim of this proposal is to establish in vivo the combinatorial effects of chromatin modifiers and transcription factors on model loci in human cells, and to unambiguously characterize by novel genetic and biochemical analyses, the resulting histone "marks" associated with active and repressed epigenetic states. These experiments will directly test the "histone code" hypothesis. Moreover, the implications of this research for human biology and health research are potentially far reaching.