Epigenetic regulation of neuronal regeneration after spinal cord lesion in zebrafish

Supervisors: Thomas Becker, Alasdair MacKenzie

Project description:


In contrast to mammals, zebrafish regenerate spinal neurons after injury (Becker and Becker, 2015). These new neurons replace lost ones and act as relays to bring about functional recovery. This is never observed in mammals. It is therefore important to determine how gene expression programmes change in spinal progenitor cells after injury to allow for neurogenesis in zebrafish. In this PhD project in the Becker group (Edinburgh), the student will elucidate the epigenetic determinants of regenerative neurogenesis. The Becker group have established an efficient larval regeneration paradigm (Wehner et al., 2017) and preliminary observations indicate that epigenetic histone acetylation levels are altered after a lesion. Low acetylation levels are necessary for proper regeneration of motor neurons.


Based on these functional data the student will use bioinformatics approaches with the MacKenzie group (Aberdeen) to identify target sequences and downstream genes of these alterations of acetylation (Hay et al., 2017). The importance of downstream genes will then be verified by in vivo perturbation experiments in zebrafish using CRISPR/Cas9 knock out and cell-type specific over-expression using the TetOn system. The student will work with a postdoc Dr Leonardo Cavone, funded by a new BBSRC project grant (to Thomas Becker, start date 15.10.2017).

With this line of research, we hope to elucidate the intrinsic changes in spinal stem cells necessary for successful spinal cord regeneration. This project will provide targets for manipulations in endogenous mammalian stem cells, which invariably fail to generate neurons after injury.

Training outcomes

The student will be trained in complex cloning techniques, in vivo perturbations and analyses using the zebrafish system, confocal imaging techniques and bioinformatics approaches applied to systems biology.


The student will be based in the Becker group in Edinburgh’s Centre for Discovery Brain Sciences (formally CNR). Bioinformatics training will be delivered in Aberdeen in the MacKenzie group. Dr MacKenzie will travel to Edinburgh for 10 week and progression meetings and there will be regular progress meetings via skype (as needed).


Becker, C. G. and Becker, T. (2015). Neuronal regeneration from ependymo-radial glial cells: cook, little pot, cook! Dev Cell 32, 516-527.

Hay, E. A., Cowie, P. and MacKenzie, A. (2017). Determining Epigenetic Targets: A Beginner's Guide to Identifying Genome Functionality Through Database Analysis. Methods in molecular biology (Clifton, N.J.) 1589, 29-45.

Wehner, D., Tsarouchas, T. M., Michael, A., Haase, C., Weidinger, G., Reimer, M. M., Becker, T. and Becker, C. G. (2017). Wnt signaling controls pro-regenerative Collagen XII in functional spinal cord regeneration in zebrafish. Nat Commun 8, 126.