Chris Ponting Research Group
Causal variants and mechanisms in complex traits and diseases
Section Head: Biomedical Genomics
Research in a Nutshell
The challenge in genomics is to pinpoint DNA variants that alter individuals’ risk to common disease; the challenge in genetics is to determine how these changes alter genetic mechanisms; and, the challenge in cell biology is to find out how these altered mechanisms affect development, cells and organs. Our research uses cutting-edge analytical approaches in genomics, transcriptomics, and cell biology to trace the causal links relating DNA variation to physiological outcome. Our research intersects disease genomics, computational biology, machine learning and molecular mechanism.
We are currently pursuing two major research projects:
- Disease and trait genomics. Blending single cell and functional genomics analysis, and machine learning, we predict molecular mechanisms by cell type and developmental stage. We then determine whether DNA variants altering these mechanisms influence human traits, including diseases. This research contributes to MRC’s strategy to investigate biological complexity in real life and at different scales and UKRI’s Delivery Plan to understand today’s greatest challenges that span society and cross disciplinary boundaries. This project is providing a vibrant and eclectic training environment for PhDs and postdocs from diverse backgrounds.
- ME/CFS Genetics. Funded by MRC and NIHR, we are part of DecodeME, the world’s biggest genetic study of the causes of ME/CFS. This project is a co-production between academics, people with ME and carers. We have also received PhD funds to investigate whether people with ME differ in their T-cell repertoire from healthy controls (funded by Action for M.E. and the Scottish Government’s Chief Scientist’s Office) and to follow-up leads from the DecodeME study (funded by ME Research UK). We support Action for ME’s vision to establish ME/CFS’s first Genetics Centre of Excellence.
Other aspects: The group also contains: Dr Jeanette Baran-Gale, who is undertaking transcriptomic analysis of single thymic epithelial cells to discover how they express nearly all protein-coding genes (with Prof Georg Hollander); Dr Luis Sanchez-Pulido detects deep homology relationships that immediately provide experimentally testable functional hypotheses;
|Professor Chris Ponting||Group Leader|
|Tom Baker||Data Manager, DecodeME|
|Jeanette Baran-Gale||Research Fellow|
|Joshua Dibble||PhD Student|
|Lyndsey Fletcher||PhD Student|
|DecodeME Project Manager|
|Abel Jansma||PhD Student|
|Cristina Martin||X-net Project Manager|
|Gosia Migdal||DecodeME Admin Manager|
|Gemma Samms||PhD Student|
|Luis Sanchez-Pulido||Research Fellow|
|Jareth Wolfe||Research Fellow|
- Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F, Sit RV, Neff NF, Darmanis S, Tan W, May AP, Marioni JC, Ponting CP*, Holländer GA*. (2020) Ageing compromises mouse thymus function and remodels epithelial cell differentiation. eLife 9:e56221
- Dhalla F, Baran-Gale J, Maio S, Chappell L, Holländer GA*, Ponting CP*. (2020) Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells. EMBO J 39:e101828
- Sirey TM*, Roberts K, Haerty W, Bedoya-Reina O, Rogatti-Granados S, Tan JY, Li N, Heather LC, Carter RN, Cooper S, Finch AJ, Wills J, Morton NM, Marques AC, Ponting CP*. (2019) The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity. eLife 8:e45051
- Bretherick, A.D., Canela-Xandri, O., Joshi, P.K., Clark, D.W., Rawlik, K., Boutin, T.S., Zeng, Y., Amador, C., Navarro, P., Rudan, I., Wright, A.F., Campbell, H., Vitart, V., Hayward, C., Wilson, J.F., Tenesa, A., Ponting, C.P., Baillie, J.K., Haley, C. (2020) Linking protein to phenotype with Mendelian Randomisation detects 38 proteins with causal roles in human diseases and traits. PLoS Genet. 16: e1008785.
- Kousathanas, A., Pairo-Castineira, E. et al. (including Ponting, C.P.) Caulfield, M.J., Baillie, J.K. Whole-genome sequencing reveals host factors underlying critical COVID-19. (2022) Nature
Full publication list can be found on Research Explorer: Chris Ponting — University of Edinburgh Research Explorer
- Professor Georg Hollander, University of Oxford
- Dr Ava Khamseh & Dr Sjoerd Beentjes, University of Edinburgh
Partners and Funders
- Action for ME/ Chief Scientist's Office, Scotland
- ME Research UK
Population genomics, long non-coding RNA mechanism, molecular mechanisms in complex disease.
Single cell biology