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Super-resolution imaging of maturing heterochromatin states in developing embryos and stem cells(co-second supervisor, Dr Sari Pennings, University of Edinburgh)

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  • Full or part time
    Prof R Meehan
    Prof R Duncan
  • 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:
The appearance of nuclear heterochromatin in mouse embryogenesis coincides with differentiation and a restriction in developmental potential, yet its causal involvement in these processes remains unclear. Derivation of embryonic stem cells (ESC) from the embryo inner cell mass (ICM) results in their adoption of DAPI positive heterochromatin, and acquisition of high levels DNA methylation and repressive histone modifications that are not detectable in the early ICM1. We have induced a reduction in heterochromatin in ESCs by lowering DNA methylation and H3K27me3 levels under ground-state conditions, resulting in nuclear morphologies resembling those of 2-cell embryos2. We wish to analyse these dynamic chromatin transition states by high-resolution imaging of ESCs and early embryos in combination with fluorescent sensors of H3K27me3 and other chromatin modifications and DNA methylation, using antibodies, tagged constructs and 3D FISH along with DAPI staining. Using 3D structured illumination microscopy (SIM), we could resolve distinct DNA-dense nuclear foci in somatic cells that suggest DAPI positive DNA methylated heterochromatin constitutes a higher order assembly, independent from H3K27me3 blocks. Our hypothesis, based on our recent molecular findings, is that these structures are further resolvable using combined super-resolution imaging technologies (SIM, 3D-STORM, g-STED), and may be found to become more interchangeable under testable epigenetic disruption conditions (inhibitors, culture conditions and genome editing). Their assembly/disassembly will be followed (e.g., by time lapse imaging; FLIM/FRET interaction status) in our ground state ESC and early embryos3,4. We will further test the hypothesis that the occurrence of heterochromatin in development is indicative of a loss of cell potency and this will be reflected in altered expression states. The project will combine cutting-edge 3D imaging at the ESRIC facilities, embryology, ESC model systems, epigenetics analysis methods and bioinformatics; in a PhD study bridging molecular investigations and nuclear super-resolution imaging.

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 protected]

Applicants must also submit an online application, to our PhD programme via EUCLID following the instructions at http://www.igmm.ed.ac.uk/students/recruitment/
We will not consider applications that have not been submitted to both [email protected] 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 protected] and further information and eligibility requirements are available at http://www.igmm.ed.ac.uk/students/

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.


1. Wongtawan, T., Taylor, J.E., Lawson, K.A., Wilmut, I., and Pennings, S. (2011). Histone H4K20me3 and HP1alpha are late heterochromatin markers in development, but present in undifferentiated embryonic stem cells. J Cell Sci 124, 1878-1890.

2. Ishiuchi, T., Enriquez-Gasca, R., Mizutani, E., Boskovic, A., Ziegler-Birling, C., Rodriguez-Terrones, D., Wakayama, T., Vaquerizas, J.M., and Torres-Padilla, M.E. (2015). Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly. Nat Struct Mol Biol 22, 662-671.

3. Reddington, J.P., Perricone, S.M., Nestor, C.E., Reichmann, J., Youngson, N.A., Suzuki, M., Reinhardt, D., Dunican, D.S., Prendergast, J.G., Mjoseng, H., et al. (2013). Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol 14, R25.

4. Reddington, J.P., Sproul, D., and Meehan, R.R. (2014). DNA methylation reprogramming in cancer: does it act by re-configuring the binding landscape of Polycomb repressive complexes? Bioessays 36, 134-140.

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