Analysis of TDG Dependent Ribonucloprotein Complex formation on Long Noncoding RNA by SILAC
Research Project
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01.06.2016
- 31.08.2016
The generation of a diversity of cells with different functions is crucial for multicellular organisms. The individual cell identity relies on a selective readout of the genome achieved with the help of epigenetic mechanisms which direct the transcriptional programs to cell-type specific endpoints. Working at the level of chromatin, these mechanisms orchestrate gene transcription by deposition, exchange or removal of epigenetic modifications at histones as wells as in the DNA. Inaccuracy of the epigenetic system not only impedes successful establishment of cell identity but may also have deleterious effects on tissue homeostasis. This is best exemplified by epigenetically unstable cancers which frequently show aberrant patterns of CpG methylation. Thus, a faithful control of the epigenetic machinery is critical for the preservation of correct cell identity. We have identified Thymine DNA glycosylase as a potential epigenetic proof-reader in CpG rich promoters of genes in active and bivalent chromatin. TDG helps to maintain these regions in an unmethylated state by initiating a DNA repair process at sites of erroneous cytosine methylation. Research of the last years has shed light on how TDG dependent active demethylation may occur at the molecular level; yet, the ways how this process is regulated and targeted to its site of actions remain obscure. Hints on how this may be achieved come from knowledge obtained for long noncoding RNAs. Serving as scaffolds, some of these RNAs have been shown to play a central role for the regulation of epigenetic processes. Together with our own preliminary data showing association of TDG with a variety of lncRNAs this suggests that these RNAs may be important for TDG mediated active DNA demethylation. Intriguingly, previously identified interaction partners of TDG, such as e.g. nuclear receptors have been reported to associate with some of the identified TDG bound lncRNAs, especially steroid receptor RNA activator 1. The work proposed herein will follow-up on this important question and investigate the TDG dependent composition of ribonucleoprotein complex by SILAC using SRA1 as a model lncRNA.
