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MRC DiMeN Doctoral Training Partnership: Single-molecule insights into an age-old problem: determining how Shelterin safeguards telomere structure and stability


   MRC DiMeN Doctoral Training Partnership

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  Dr A Pyne, Dr S Boulton, Dr Matthew Newton  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Background:

Telomeres solve two problems with linear chromosome ends: the end-replication problem, DNA loss from the end of chromosomes every replication cycle; and the end-protection problem, protection of chromosome ends to prevent chromosome fusions. Telomere homeostasis is vital, as mutations in telomeric complexes drive cancer development and accelerate ageing due to dysregulated telomere lengthening or shortening. Shelterin, a large protein complex, binds to telomeres and is central to maintaining telomere homeostasis. This project will use our recently developed in vitro reconstituted telomeric system to determine how Shelterin orchestrates multiple telomere activities at the single-molecule and cellular level. This approach will for the first time directly observe telomeric DNA structure, down to the resolution of the double-helix, whilst allowing direct monitoring the activity of individual Shelterin complexes.

Objectives:

1.    Generate telomeric substrates containing G-quadruplexes or R-loops

2.    Determine how different telomeric structures effect activity of Shelterin at the single-molecule level

3.    Probe how differences in Shelterin activity affect T-loop stability and end-protection in vivo

Novelty:

Ageing is a primary driver of some of the most prevalent chronic diseases including Alzheimer’s and cancers. Understanding the physiological mechanisms of ageing could prevent a wide variety of diseases. A lack of a reconstituted telomeric system means fundamental mechanistic details remain unknown. We have successfully purified the entire Shelterin complex and demonstrated that it is active, enabling reconstitution of Shelterin mediated telomere function in vitro. We have developed single-molecule experimental approaches tailored to this project with leading industrial partners (Bruker, Lumicks). This will facilitate the first direct visualisation of Shelterin recruitment and end-protection activities, giving unprecedented insight into how Shelterin modulates these processes.

Experimental Approach:

This project combines multiple cutting-edge single-molecule techniques, and the expertise of leaders in these fields, to directly visualise telomeric processes. In this project you will receive training in high-resolution AFM which will enable you to visualise different telomeric DNA structures down to the resolution of the double-helix. You will use and develop our open quantitative image analysis tools, integrating machine learning approaches to visualise and quantify structural features within Shelterin bound telomeric DNA. You will observe dynamic Shelterin activity on telomeric DNA at single-molecule resolution using our optical-tweezers setup which is combined with confocal microscopy. These biophysical approaches will be supported by established cellular and genetic assays to validate findings in vivo. Finally, we will characterise cancer and ageing associated mutations to understand how they dysregulate telomere function.

You will be supervised by Dr Alice Pyne, a senior lecturer at the University of Sheffield, Prof Simon Boulton, a principal group leader at the Francis Crick Institute and Dr Matt Newton, a Wellcome Fellow based across the two groups. All supervisors are committed to embedding positive and inclusive research cultures in their groups. The supervisors will work together to ensure expectations on students and of supervisors are clearly defined and communicated.

We welcome applicants from a diverse range of backgrounds across the physical and biological sciences and engineering. Interested applicants should contact [Email Address Removed].

Twitter: @alicepyne, @BoultonLab, @M_D_Newton

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: https://www.dimen.org.uk/blog

Further information on the programme and how to apply can be found on our website:

https://www.dimen.org.uk/how-to-apply


Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 4yrs. Funding will cover tuition fees, stipend and project costs. We also aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of full studentships to international applicants. Please read additional guidance here: https://www.dimen.org.uk/eligibility-criteria
Studentships commence: 1st October 2023
Good luck!

References

Anand, R. et al. HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51. Nature 601, 268–273 (2022).
Pyne, A. L. B. et al. Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nature Communications 12, 1053 (2021).
Newton, MD. et al. DNA stretching induces Cas9 off-target activity. Nature Structural & Molecular Biology 26, 185–192 (2019).
Ruis, P. et al. TRF2-independent chromosome end protection during pluripotency. Nature 589, 103–109 (2021).
Beton, J. G. et al. TopoStats – A program for automated tracing of biomolecules from AFM images. Methods 193, 68–79 (2021).
Akpinar, B. et al. PEGylated surfaces for the study of DNA–protein interactions by atomic force microscopy. Nanoscale 11, 20072–20080 (2019).
Sarek, G. et al. CDK phosphorylation of TRF2 controls t-loop dynamics during the cell cycle. Nature 575, 523–527 (2019).
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