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New super-resolution techniques for investigating chromatin architecture in mammalian cells

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  • Full or part time
    Prof N Gilbert
    Dr J Arlt
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

ESRIC PhD Programme:

This is one of four projects being offered in 2016 for one three-year PhD studentship available in the Edinburgh Super-resolution Imaging Consortium (ESRIC), aiming to apply state-of-the-art microscopy techniques to investigate cellular function and human disease. ESRIC is one of the most comprehensively equipped super-resolution Centres of Excellence in Europe, with state-of-the-art systems alongside a broad range of expertise across the scientific spectrum. This is an exciting opportunity to work at the cutting edge of biological imaging at the molecular scale with access to the latest technology. Appropriate multi-disciplinary supervision will be provided.

Project description:
In mammalian cells DNA is precisely folded with proteins to form a macromolecular complex called chromatin. Chromatin both protects the genome from damage but is also the substrate for nuclear processes such as replication, transcription and repair. Despite significant research the folding of chromatin in the nucleus is extremely controversial. Many studies argue chromatin is folded into a 30-nm fibre that is further compacted into higher order structures, but an alternate view suggests that chromatin is arranged as a 10-nm fibre, forming fractal globules. Super-resolution microscopy has started to be used to probe chromatin structure in mammalian cells (Ricci et al., 2015) but has not provided a definitive answer to how chromatin is organised and regulated. In this PhD project we will develop new super-resolution approaches to investigate the organisation of chromatin in mammalian cells.

Live cell imaging has many advantages over fixed samples but the sensitivity and speed of many super-resolution techniques precludes this, necessitating sample fixation. Historically formaldehyde has been used as the fixative of choice however it is not ideal; it forms very extensive short cross-links (2-3 Å) potentially altering the structure of features being studied. As this is a severe issue for super-resolution microscopy, we have developed a series of UV-activated protein-DNA and DNA-DNA cross-linkers. To optimise the use of these cross-linkers the student will investigate first by SIM, and then by PALM/STORM the organisation of heterochromatin in wild type mouse embryonic stem (ES) cells and ES cells that have mutations in proteins important for regulating heterochromatin structure (e.g. SUV39H1, DNMT3A) (Gilbert et al., 2007; Bruton et al. (unpublished)). ES cells will also be differentiated to neural precursors triggering a major re-organisation of chromatin, providing further insight into the dynamic regulation of chromatin architecture. Using ES cell heterochromatin as an experimental system we will investigate how heterochromatin is organised compared to euchromatin in optimally fixed cells to understand the nature and organisation of higher-order chromatin fibres.

In this project the student will optimise a novel family of cross-linkers for super-resolution microscopy and develop a super-resolution SPIM platform suitable for imaging chromatin. Using these optimised super-resolution approaches the student will investigate the re-organisation of chromatin during embryonic stem cell differentiation and in ES cell genetic mutants lacking key heterochromatin proteins to gain novel insight into the folding and organisation of chromatin fibres.

Who should apply:
The Edinburgh Super-Resolution Imaging Consortium PhD programme is highly multi-disciplinary, attracting students with a diverse range of backgrounds including first degrees in STEM subjects (biology, biochemistry, genetics, chemistry, physics, and engineering).

How to Apply:
Applicants should hold at least an upper second class degree or equivalent in a related subject. Applicants should submit a personal statement about your research interests, reasons for applying and a C.V. before 28 February to [Email Address Removed].

Applicants must also submit an online application, to our PhD programme via EUCLID following the instructions at
We will not consider applications that have not been submitted to both [Email Address Removed] and EUCLID by the closing date.

If you have not heard from us by 7 March please consider your application unsuccessful (we will not be able to provide feedback on unsuccessful applications).

Shortlisted candidates will be invited to attend interview in early April. General enquiries can be made to: [Email Address Removed] and further information and eligibility requirements are available at

This funded studentship is open only to UK students, or EU students if they have been studying in the UK for the previous 3 years or working in a related discipline in the UK. EU students coming from a discipline related to super-resolution imaging are also eligible to apply.

Further information:

Funding Notes

Funding: The MRC HGU will be funding one ESRIC PhD studentship through the University of Edinburgh for 2016 application. Each studentship is funded for 3 years. This includes tuition fees, stipend and bench fee.
Stipend: Students receive a tax-free stipend of at least £17,350 per year.
Bench fees: A generous allowance is provided for research consumables and for attending UK and international conferences.


Gilbert N, et al. DNA methylation affects nuclear organization, histone modifications, and linker
histone binding but not chromatin compaction. J Cell Biol. 2007 177(3):401-11
Ricci MA, et al. Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell. 2015 160(6):1145-58.
Zhao ZW, et al. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet super-resolution microscopy. Proc Natl Acad Sci U S A. 2014 111(2):681-6.

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