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Enabling large population-based epigenetic studies in livestock and comparative epigenomics

College of Medicine and Veterinary Medicine

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Prof A Tenesa , Dr P Navarro , Dr J Prendergast No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Epigenetic variation, especially DNA methylation (mDNA) has been linked to infectious and non-infectious disease in humans. This evidence is both at global (i.e. whole epigenome) and gene level.
Across livestock species, there is also evidence that mDNA levels mediate various important production traits of economic value. For example, global blood mDNA levels have been associated with milk production differences in dairy cows1, and body size associated CpG sites have been uncovered in sheep2 but so far studies are based on relatively few individuals and are often not (epi)genome-wide.

Despite the evidence that mDNA is associated with phenotypic variation across species, there are no comprehensive comparative studies, partly due to that fact that, unlike for humans, there are no cost-effective methods to perform large population studies in livestock.

This studentship aims to facilitate these across species comparative studies by investigating in depth differences and similarities in, for example, location and genomic context of CpG sites across species. Previous work3 has shown that, for subsets of CpG sites, human-mouse homology is greater in genic regions, where sequence conservation is high, than for enhancers. We will create an extensive comparative map assessing homology of the mDNA landscape within different annotations. This research will ultimately facilitate the development of new arrays that survey mDNA efficiently and cost-effectively in livestock. These could then be applied to further investigate at scale the role of DNA methylation in health, production and adaptation in large livestock populations, and enable comparative epigenetic studies.

The proposed research will require the bioinformatic analysis of large sequence data across species (humans, sheep and cattle primarily) and breeds. The project will heavily rely on bioinformatics knowledge and strong computational and analytical skills and hence will suit a student that has or is interested in further developing these.

Funding Notes

3.5 year PhD

This opportunity is open to UK and international students and provides funding to cover stipend, tuition fees and consumable/travel costs. Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to [Email Address Removed].

When applying for the studentship please state clearly the project title/s and the supervisor/s in your covering letter.

Other projects available:
We would encourage applicants to list up to three projects of interest (ranked 1st, 2nd and 3rd choice) from those listed with a closing date of 10th January 2021 at


1. Wang, L., Sun, H.Z., Guan, L.L. & Liu J.X.(2019) Relationship of blood DNA methylation rate and milk performance in dairy cows. Journal of Dairy Science.
2. Cao, J., Wei, C., … & Du, L. (2015). DNA methylation Landscape of body size variation in sheep. Scientific reports.
3. Needhamsen, M., Ewing, E., Lund, H., Gomez-Cabrero, D., Harris, R. A., Kular, L., & Jagodic, M. (2017). Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies. BMC bioinformatics, 18(1), 486.
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