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MRC Precision Medicine DTP: 3D modelling of changes in genome architecture in development and disease

  • Full or part time
    Prof E Schirmer
    Dr D Marenduzzo
  • Application Deadline
    Monday, April 08, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Background
Defects in spatial genome organisation have recently been linked to human disease and the National Institutes of Health, USA director speculated that most as yet unidentified disease alleles will occur in non-coding genome regions. Genome organisation changes during differentiation generate tissue-specific spatial patterns of gene positioning that contribute to gene expression regulation. We identified several tissue-specific nuclear envelope transmembrane proteins (NETs) that direct tissue-specific gene repositioning. We used genome-wide approaches to map genome regions located at the nuclear periphery during myogenesis, adipogenesis, in liver, and during lymphocyte activation1-3. In each system important differentiation/metabolic genes fail to reposition/regulate expression with loss of the particular tissue-specific NET with an inhibition of tissue differentiation1. Tethering at the nuclear envelope of regions flanking and slightly distal to genes can influence the ability of these genes to associate with superenhancers to achieve higher levels of expression3. Accordingly, we generated Hi-C datasets for changes in internal genome organisation during myogenesis to elucidate how nuclear envelope tethering influences internal genome interactions and is altered in disease states. We recently sequenced several unlinked cases of Emery-Dreifuss muscular dystrophy (EDMD) and found mutations in the muscle-specific NETs that direct myogenic genome organisation changes and have obtained an MRC grant to investigate the effects of these mutations on muscle function and pathology in mice. We separately generated a fat-specific NET knockout mouse that has a lipodystrophic phenotype, suggesting that NET-directed genome organisation may contribute to many diseases. Previous work modeling genome organisation changes with genome engineered mutations has revealed mechanistic insights into cell state conditions4 and we expect similar modeling for EDMD will lead to better understanding this disorder.
Aims
1. Point mutations found in muscle-specific NETs that function in genome organisation will be tested in both tissue culture and mice for how they alter genome organisation and their effects on muscle development, metabolic function, and pathology to clarify their functioning as EDMD disease alleles and elucidate mechanism of disease pathology.
2. As several genes regulated by muscle NETs are also needed for muscle regeneration, the student will test their effects in tissue damage-repair mechanisms. Muscle damage will be effected using notexin and changes in gene positioning, gene expression, and muscle metabolism determined.
3. Genome editing will be engaged to study specific loci and the effects of their disruption independent of muscle NET function. Enzymatically dead CRISPR/Cas9 will be fused to a widely expressed NET and cells made to stably express guide RNAs to a particular critical gene locus so that this locus can be maintained at the periphery when it is normally released and needed.
4. The student will model data together with physicist collaborator Davide Marenduzzo to generate 4D genomic maps of nuclear organisation. This data will ideally be transformed into a visual interface to use also for outreach so that young students can easily visualise the changes in gene positioning and activation that take place in muscle development and how they are disrupted in disease.
Training outcomes
The student will learn to produce and analyse genome-wide DamID, Hi-C and RNA-Seq data through supervision from the Schirmer lab bioinformatician, the Wellcome Centre Bioinformatics Core, and our collaborator Job Dekker (University of Massachussetts, USA), while confirming specific results through fluorescence in situ hybridisation and 3C. The student will also learn CRISPR/Cas9 genome editing approaches in association with the post-doc and technician on the MRC grant and with use of the CRISPR users groups. The student will ideally also get their personal animal license (PIL) to assist in mouse studies. Finally, the student will learn modeling with collaborator Marenduzzo to generate 4D genome organisation maps.

This MRC programme is joint between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection.

All applications should be made via the University of Edinburgh, irrespective of project location: http://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=919

Please note, you must apply to one of the projects and you should contact the primary supervisor prior to making your application. Additional information on the application process if available from the link above.

For more information about Precision Medicine visit: http://www.ed.ac.uk/usher/precision-medicine
https://www.ed.ac.uk/usher/precision-medicine/project-opportunities


Funding Notes

Start: September 2019

Qualifications criteria: Applicants applying for a MRC DTP in Precision Medicine studentship must have obtained, or will soon obtain, a first or upper-second class UK honours degree or equivalent non-UK qualifications, in an appropriate science/technology area.

Residence criteria: The MRC DTP in Precision Medicine grant provides tuition fees and stipend of at least £14,777 (RCUK rate 2018/19) for UK and EU nationals that meet all required eligibility criteria.

Full eligibility details are available: View Website

Enquiries regarding programme:

References

1. Robson, M. I., de las Heras, J. I., Czapiewski, R., Le Thanh, P., Booth, D. G., Kelly, D. A., Webb, S., Kerr, A. R. W., and Schirmer, E. C. (2016) Tissue-specific gene repositioning by muscle nuclear membrane proteins enhances repression of critical developmental genes during myogenesis. Mol. Cell 62(6), 834-847. PMID: 27264872
2. de las Heras, J. I., Zuleger, N., Batrakou, D. G., Czapiewski, R., Kerr, A. R. W., and Schirmer, E. C. (2017) Tissue-specific NETs alter genome organization and regulation even in a heterologous system. Nucleus 8(1), 81-97. PMID: 28045568
3. Robson, M. I., de las Heras, J. I., Czapiewski, R., Sivakumar, A., Kerr, A. R. W., and Schirmer, E. C. (2017) Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments. Genome Res doi: 10.1101/gr.212308.116. PMID: 28424353
4. Zirkel, A., Nikolic, M., Sofiadis, K., Mallm, J.P., Brackley, C.A., Gothe, H., Drechsel, O., Becker, C., Altmüller, J., Josipovic, N., Georgomanolis, T., Brant, L., Franzen, J., Koker, M., Gusmao, E.G., Costa, I.G., Ullrich, R.T., Wagner, W., Roukos, V., Nürnberg, P., Marenduzzo, D., Rippe, K., Papantonis, A. (2018) HMGB2 loss upon senescence entry disrupts genomic organization and induces CTCF clustering across cell types. Mol Cell 70(4):730-744.e6. doi: 10.1016/j.molcel.2018.03.030. PMID: 29706538

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