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

  • Full or part time
    Dr M Wilson
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

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





Funding Notes

The “Visit Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process. Follow the instructions on the EASTBIO website (you will be directed here from our application checklist), ensuring you upload an EASTBIO application form and transcripts to your application, and ticking the box to request references. Your referees should upload their references using the EASTBIO reference form, in time for the 5th January deadline so please give them plenty of time to do this by applying early.

References

Wilson MD, Costa A. (2017) Cryo-electron microscopy of nucleosome biology. Acta Cryst D. D73, 541-548

Muller, L. S. M. et al. Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature 563, 121-125, doi:10.1038/s41586-018-0619-8 (2018).

Koyama, M., and Kurumizaka, H. (2018). Structural diversity of the nucleosome. J Biochem 163, 85-95.

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

Research output data provided by the Research Excellence Framework (REF)

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