CAC-seq. · Chemical assisted enrichment of 5-carboxycytosine that also allows for DNA sequencing at single base resolution.
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2020-04-01 → 2022-03-31
- EU contribution
- €212,934
- Participants
- 1
- Scheme
- MSCA-IF
Lines connect the coordinator with its partners.
Results in brief
Chemical assisted enrichment of 5-carboxycytosine that also allows for DNA sequencing at single base resolution.
Next-generation sequencing constitutes a powerful tool to analyze genomic material at unprecedented depth and scale to detect disease-specific mutations. Besides changes in the canonical base sequence epigenetically modified cytosine derivatives have also been linked to various disease states. Chemical and enzymatic methods that selectively target epigenetic markers are central to study their distribution and function with the help of nucleic acid sequencing. During the course of this action, a photochemical method for the conversion of epigenetic 5-carboxycytosine (5caC) to a T-like base has been developed that allows for base resolution sequencing of 5caC. In addition, the developed chemistry can also be applied to sequence 5-methylcytosine (5mC) in genomic DNA. The methodology could be used in diagnostic applications for the early detection of deadly diseases such as cancer.
Data: CORDIS, © European Union
Project 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.
Original text from CORDIS.
Participants
- THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE · CAMBRIDGECoordinatorUnited Kingdom
Links
Data: CORDIS, © European Union