Prof. Beat Fierz: Laboratory of Biophysical Chemistry of Macromolecules
Prof. Bart Deplancke, Laboratory of Systems Biology and Genetics
Gene expression is directed by enhancer regions, which are segments of DNA that can be located quite far from the genes they control. The 3D arrangement of DNA in the cell nucleus, which exists in a complex with proteins forming chromatin, brings enhancers close to their target genes, but the exact way this happens is not well understood. It is very challenging to directly observe how specific DNA sequences are organized in the dense environment of a cellular nucleus without damaging them. Current techniques to study specific DNA locations indeed involve methods relying on thermally melting the DNA and thus disrupt the local structure.
To overcome these challenges, profs. Beat Fierz and Bart Deplanck in collaboration with prof. Aleksandra Radenovic started working on creating new ways to see how DNA is structured at the level of individual genes and their associated control regions, i.e. enhancers. Through this collaborative grant, they developed a technology for metabolic incorporation of a tagged DNA nucleotide -organic molecule that forms the basic unit of nucleic acids into long DNA constructs in bacteria, followed by direct chemical labelling and imaging. Researchers developed a way to incorporate a tagged nucleotide, AmdU, into bacterial DNA and then label it using a special dye that binds efficiently to DNA. Further optimization is needed to improve resolution for chromatin imaging and integrate the labeled DNA into cells effectively, but the initial imaging tests show promise.
In the coming months, this technology will be tested on a specific gene involved in a type of leukemia -AXIN2 locus-, to see how enhancers change shape in different conditions. Currently, scientists established a fully functional workflow, allowing them to measure the transcriptional output of both promoter, enhancer, as well as simultaneous promoter-enhancer manipulations. By integrating libraries of synthetic enhancers that harbor a combination of different transcription factor (TF) binding sites (BSs) into the endogenous locus, they were able to learn new mechanistic insights into enhancer communication. Critical experimental hurdles are overcome and the combination of DNA and cellular engineering methods to achieve chromatin imaging in living cells has yet to be achieved.
