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Using computational approaches to decode epigenetic control in transcription regulation

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  • Full or part time
    Dr Chen
    Prof David Westhead
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

Gene expression regulation is tightly regulated to ensure normal cellular physiology during development and in response to stress. An important process to control gene expression is chromatin regulation. Histone proteins form part of chromatin, which can be modified by chromatin modifiers and the changes on the histone tails can alter the structure of chromatin, resulting in the activation or repression of gene activity. Misregulation of these modifications can lead to the onset of human diseases such as cancer and developmental defects. Therefore, it is essential to improve our knowledge in the fundamental regulatory mechanisms that would be the target for developing novel treatments.

My previous work demonstrated that humans and C. elegans share similar promoter-enhancer architectures. It makes the latter a powerful genetic model organism to study promoter-enhancer regulation that is relevant to human diseases. In addition, the high degree of conservation in the chromatin landscape and protein factors, plus the ease of genetic/molecular experiments make C. elegans an attractive model to study transcription regulation at the organismal level.

We are interested in investigating the novel function of chromatin modification complexes in stress-induced gene expression programmes using functional genetics and “omics” approaches. We have recruited two PhD students to work on the “wet” experiments. To strengthen our research programme, we are inviting PhD student applicants with proven ability in programming languages (e.g. R and/or Python); previous experience in analysing omics data sets would be a bonus. This bioinformatics studentship post will be collaborative and interdisciplinary and requires a mind with strong curiosity and a passion for answering biological questions. The candidate will benefit from an interactive and supportive working environment to explore the world of epigenetic control.

The candidate will have stimulating interactions with biochemists, structural biologists and geneticists to receive a comprehensive training and support through the PhD project in the School of Molecular and Cellular Biology at Leeds.

We are inviting applicants with a good degree in natural sciences and with a strong ability in computing programming (e.g. R and/or Python) and passion for computational biology.

If you wish to enquire further details of the project informally, please contact Dr. Ron Chen, email: [email protected]

Our lab webpage is: http://www.RonChenLab.info


Funding Notes

We would support outstanding applicants to compete for Commonwealth Scholarships (http://cscuk.dfid.gov.uk/apply/scholarships-developed-cw/).

References

The modENCODE consortium. (2014) Comparative analysis of metazoan chromatin organization. Nature 512(7515):449-452.

Chen R.A.-J., Stempor P., Down T.A., Zeiser E., Feuer S. and Ahringer J. (2014) Extreme HOT regions are CpG dense promoters in C. elegans and humans. Genome Research 24(7):1138-1146.

Weick, E.-M.*, Sarkies, P.*, Silva, N., Chen, R.A.-J., Moss, S.M.M., Cording, A.C., Ahringer, J., Enrique Martinez-Perez, E and Miska, E. (2014) PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif dependent piRNAs in C. elegans. Genes Dev 28(7):783-796.

Chen R.A.-J*., Down T.A*., Stempor P., Chen, Q.B., Egelhofer T.A., Hillier L.W., Jeffers T.E. , Ahringer J.A. (2013) The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Research 23(8):1339-1347.

How good is research at University of Leeds in Biological Sciences?

FTE Category A staff submitted: 60.90

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