From Live Cells to Single-molecules: Unravelling the interplay between 3D genomic structure and gene expression

This studentship is focused on applying state-of-the-art single molecule imaging techniques to study the molecular basis of DNA condensation and its impact upon gene expression. You will be part of a new, multidisciplinary collaboration between the Dept. of Oncology and Metabolism and Dept. of Chemistry with close ties to the Sheffield Institute for Nucleic Acids (http://genome.sheffield.ac.uk/).

Human cells must pack ~2 metres of DNA in to a cell nucleus approximately 10um in diameter. The DNA must be packaged yet, highly organised and accessible for gene expression, DNA replication and DNA repair machinery. The 3D organisation also changes over time in response to cell stimulation such as DNA damage or infections. Central to this organisation is the wrapping of DNA around histone proteins to form nucleosomes that can be packed (condensed) or unpacked to allow proteins to access the genome. An array of modifying enzymes regulate these processes.

We have recently identified NDP52/CALCOCO2 as a putative transcription regulator (1) and preliminary data shows that this protein decondenses nucleosomes. NDP52 is connected to the NF-kB inflammation pathway and we therefore believe the protein regulates the expression of pro-inflammation genes. Therefore, this protein is related to fundamental cellular processes critical to health and disease, however it's mechanism of action remains unknown.

The goal of this project is to dissect the mechanism of DNA condensation by NDP52 through a combined cell biology and in vitro approach, identifying the roles of any interacting proteins, and therefore define the molecular mechanism underpinning this fundamental process.

You will use a "top-down" and "bottom-up" multidisciplinary approach to investigate