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Gene regulatory networks in zebrafish development


Randall Centre for Cell and Molecular Biophysics

Applications accepted all year round Self-Funded PhD Students Only
London United Kingdom Biochemistry Bioinformatics Cell Biology Developmental Biology Genetics Genomics Molecular Biology

About the Project

A PhD studentship is available to work in the laboratory of Dr. Fiona Wardle (www.kcl.ac.uk/research/profile/wardle-group) in the Randall Centre for Cell and Molecular Biophysics, King’s College London. The successful applicant will be joining a dynamic, interdisciplinary lab, within one of the world’s top research universities

Our laboratory focusses on the networks of gene regulation that control tissue and organ formation in the early vertebrate embryo, and disease progression, particularly cancer, in the adult. We use a combination of approaches to study gene regulation including cell biology, molecular biology, experimental embryology, genomics, and computational biology in a variety of systems including zebrafish, mammalian stem cells and cancer cells.

We are seeking a highly motivated and enthusiastic candidate with a background in developmental biology, biochemistry or computational biology to study gene regulatory networks in the early zebrafish embryo.

Project

This project will investigate the function of enhancer regions in regulating gene expression in zebrafish mesoderm formation. Using publicly available genomics data and 4C-seq data generated in house, the candidate will identify putative enhancer regions that regulate expression of mesodermal genes in the early embryo. The function of these will be tested using reporter assays and genome editing (CRISPR) to mutate the enhancers. The selected candidate will gain experience in zebrafish embryology, genomics, molecular biology, microscopy and bioinformatics.

Should candidates be interested in other projects in the laboratory (see: http://www.kcl.ac.uk/research/profile/wardle-group), please feel free to contact Dr Fiona Wardle for an informal discussion.

Environment

The candidate will be joining an interdisciplinary team that is based in the Randall Centre at the Guy’s Campus of King’s College London. Our group is part of a vibrant department with numerous researchers using genomics, microscopy, biophysics and computational biology to investigate development and cell biology, and the candidate will gain exposure to numerous techniques and model systems.

The Health Sciences Doctoral Training Centre will also provide methods training and opportunities for career development activities, such as presentation and writing skills (see: kcl.ac.uk/healthsciences).

Eligibility

Prospective candidates should have a 1st or 2:1 level qualification in developmental biology/biochemistry/computational biology or a related programme. Applicants are also required to meet King’s English language requirements (Band D, https://www.kcl.ac.uk/study/postgraduate/apply/entry-requirements/english-language).

To apply, please send a CV, transcript and statement of interest to Dr. Fiona Wardle ().


Funding Notes

There is currently no funding attached to this PhD call and the successful applicant will be expected to provide their own funding. We require candidates that have secured, or wish to secure, their own competitive funding from overseas government agencies or employers. King’s College London provides a list of possible schemes on the following website: View Website.

References

Representative publications from the Wardle group:

Nelson, A.C., Cutty, S.J., Gasiunas, S.N., Deplae, I., Stemple, D.L., Wardle, F.C. (2017). In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors. Cell Reports 19(13):2782-2795.

Windner, S.E., Doris, R.A., Ferguson, C.M., Nelson, A.C., Valentin, G., Tan, H., Oates, A.C, Wardle, F.C., Devoto, S.H. (2015). Tbx6, Mesp-b and Ripply1 regulate the onset of skeletal myogenesis in zebrafish. Development, 142(6):1159-68.

Nelson, A.C., Cutty, S.J., Niini, M., Stemple, D.L., Flicek, P., Houart, C., Bruce, A.E.E and Wardle, F.C. (2014). Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biology, 12(1):81.

Nelson, A.C., Pillay, N., Henderson, S., Presneau, N., Tirabosco, R., Halai, D., Berisha, F., Flicek, P., Stemple, D.L., Stern, C., Wardle, F.C., Flanagan, A.M. (2012). A gene regulatory network directed by T, brachyury gives insight into the pathogenesis of chordoma. Journal of Pathology, 228, 274-85.

Jahangiri, L., Nelson, A.C., Wardle, F.C. (2012). A cis-regulatory module upstream of deltaC regulated by Ntla and Tbx16 drives expression in the tailbud, presomitic mesoderm and somites. Developmental Biology, 37, 110-20.

Garnett, A.T., Han, T.M., Gilchrist, M.J., Smith, J.C., Eisen, M.B., Wardle, F.C., Amacher, S.L. (2009). Identification of multiple direct T-box target genes in the developing zebrafish mesoderm. Development 136, 749-60.

Morley, R.H., Lachani, K., Keefe, D., Flicek, P., Gilchrist, M.J., Smith, J.C., Wardle, F.C. (2009). A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. Proc Natl Acad Sci U S A 106, 3829-34.

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