Determine how DNA is packaged into chromatin in 3D to facilitate gene regulation

The DNA inside a cell is not randomly distributed but rather organized in a structure called chromatin. This non-random distribution has important implications for the functioning of cellular programs. The basic building block of this organisation system is the nucleosome. The nucleosome consists of a short piece of DNA wrapped around a protein core, with millions of nucleosomes are present in the cell’s nucleus. The orientation of nucleosomes with respect to each other and the way they pack the genomic DNA determine the architecture of chromatin. The 3D architecture of chromatin influences which genetic programs can be accessed at a given point in time and is, therefore, fundamental for all biological processes in the cell.

We are working to determine the 3D structure of chromatin and how it affects the regulation of gene expression. The student would work to establish relative orientations and distances between nth-nearest neighbours nucleosomes and search for patterns of chromatin geometry in large data sets defining the structure of chromatin in its distinct states. The ultimate goal of the project is to establish a streamlined pipeline for the objective mapping and measures of chromatin structure and geometry, according to variables defined during the project.