Project description
Bringing an important mammalian epigenetic modification into focus
Epigenetic changes are changes in the DNA that do not affect the DNA sequence itself. Common ones include adding a methyl group to the DNA or modification of histones, the proteins DNA wraps around to fit in the cell nucleus. They are critical to gene expression and can affect cell programming. For example, skin cells, brain cells and muscle cells contain the same DNA, but epigenetics affects which genes are turned on or off and thus cell fate. Active demethylation of DNA is important in embryonic development and in the brain, and 5-carboxylcytosine (5caC) plays a role in both cases. However, its functions are largely unknown, and it is difficult to study given its low abundance. The EU-funded CAC-seq. project is developing a powerful new method to resolve 5caC, promising significant progress in untangling its role in mammalian epigenetic outcomes.
Objective
5-carboxycytosine (5caC) has been robustly identified in mammalian DNA. It is known that this DNA modification plays a role in epigenetic demethylation processes. If 5caC has other epigenetically relevant functions is so far unknown. Due to its low abundance it is technically challenging to study this modification in biological samples. Identification of specific readers, recognition by the RNA polymerase II elongation complex, the presence in specific genomic loci as well as changing levels during differentiation of mouse embryonic stem cells (mESCs) point towards an important biological function. A chemical tool that would clarify the role of 5caC in mammalian biology is so far missing. Since DNA modifications play a significant role in human diseases, understanding their functions offer new opportunities for novel treatment strategies. Chemical tools have advanced the field enormously in detecting and analysing newly discovered modified bases by rationally designed chemistry for specific labelling of a given modification. Chemical enrichment of DNA fragments enables mapping of the bases at 200-400 base pair resolution and has been used for a genome-wide mapping of several DNA modifications. To obtain single base resolution a separate modification specific sequencing method needs to be applied after enrichment. To avoid a multistep procedure I will develop a chemical enrichment method for 5caC that is directly coupled to single base resolution sequencing. In combination this provides a powerful chemical tool that has far reaching impact for other researchers in the field and finally enables scientific progress on 5caC.
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Programme(s)
Funding Scheme
MSCA-IF - Marie Skłodowska-Curie Individual Fellowships (IF)Coordinator
CB2 1TN Cambridge
United Kingdom