EASTBIO Using cryo-EM to investigate chromatin structure in Trypanosoma brucei

Second Supervisor: David Horn, University of Dundee
We are interested in understanding how the basic unit of chromatin, the nucleosome, compacts and controls access to DNA. Different organisms have very different chromatin structures and methods to organise and use their genome, but the histones that make up the fundamental nucleosome building block are often very highly conserved. However, this is not the case for divergent eukaryotes such as trypanosomes.
Trypanosome transmission by tsetse flies is responsible for sleeping sickness in humans and Nagana in animals. Understanding how the trypanosome genome is organised and responds to stimuli is crucial for our understanding of disease. However, little is known about the structure and mechanism of DNA compaction for the highly divergent nucleosome in Trypanosomes.
Using a combination of techniques, primary structural biology approaches, we aim to determine the 3D structure of the trypanosome nucleosome and understand how DNA is compacted and used in this divergent eukaryote. We will compare the role of different epigenetic marks and histone variants allowing us to determine how the diversity in primary sequence of trypanosome histones still allows correct DNA use. By identifying common epigenetic mechanisms between trypanosome and comparing them to better-studied eukaryotic systems we can hope to understand the basic conserved rules of life. The project will involve:

1) Protein expression and purification of trypanosome histone and histone variants
2) Chemical biology technologies to generate modified histones
3) Protein biochemistry and biophysical techniques to understand the wrapping of DNA in trypanosome nucleosomes
4) Structural biology, in particular cryo-EM, to understand the molecular mechanisms of trypanosome chromatin
5) Cell biology to extend our in vitro observations to the living parasite cell

This would be an ideal project to suit a passionate, motivated student interested in how molecular understanding can help explain fundamental biological processes. Applicants must have, or expecting to be awarded, at least an upper-second class degree (or equivalent qualification) in an area of biochemical-sciences