Professor Gordon Simpson



Plant Sciences, School of Life Sciences

Portrait of Gordon Simpson
On this page




+44 (0)1382 386962




I studied cyanobacteria for my PhD at the University of Dundee with Pete Rowell and Sir William Stewart. I first worked on RNA with John Brown in collaboration with Jean Beggs from the University of Edinburgh. I won a Royal Society fellowship to join Witold Filipowicz’s lab at the Friedrich Miescher Institute, Basel, Switzerland and later joined Dame Caroline Dean’s lab at the John Innes Centre. I returned to the University of Dundee as a Lecturer, Reader, and then Professor of Molecular Genetics.



RNA processing and modification

We study RNA. Although the genes that lie in our chromosomes are made of DNA, they are transcribed into copies of RNA when they are switched on. RNA is processed and modified in ways that ultimately determine what a gene codes for. We study processing events called splicing and polyadenylation, and the modification of RNA by the addition of chemical groups. In this way, we learn what genomes really encode and how the regulation of genes leads to change in biology.

Our science is curiosity-led and attempts to answer basic questions about RNA and biology. We try to use unbiased approaches that include forward genetic screens, global sequencing of messenger RNAs and inter-species association mapping. We combine expertise in RNA molecular biology with genetics and computational biology.

Genetic screens to understand flower development led us to study RNA binding proteins that affect splicing, polyadenylation and the methylation of RNA. Although this work started with Arabidopsis, we switch experimental systems to generalise our understanding of the most fundamental questions that we can. Since sequencing RNAs reveals what genomes encode, we have partnered with the African Orphan Crop Consortium to directly sequence RNA from indigenous crops, including yam, to provide a resource to help develop future food security.

We try to be as transparent as possible in our scientific process. We freely share all our source data and the code that we use to analyse our data sets. We pre-print all our work and publish it in open-access scientific journals with transparent peer review so that anyone can read it for free. Our public engagement activities include a genetics garden that we established at the University of Dundee Botanic Garden more than 10 years ago.

Our work is publicly funded by the UK government through BBSRC and GCRF, and by the EU through Horizon 2020.

Selected Publications

Parker, M. T., Fica, S. M., Barton, G. J. & Simpson, G. G. (2023) The evolution of splice site sequence preference is linked to the U6 snRNA m6A methyltransferase METTL16. bioRxiv 2023.05.04.539401

Parker, M. T., Soanes, B. K., Kusakina, J., Larrieu, A., Knop, K., Joy, N., Breidenbach, F., Sherwood, A. V., Barton, G. J., Fica, S. M., Davies, B. H., & Simpson, G. G. (2022). m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5’ splice site. eLife, 11, e78808.

Zhang, M., Bodi, Z., Mackinnon, K., Zhong, S., Archer, N., Mongan, N. P., Simpson, G. G., & Fray, R. G. (2022). Two zinc finger proteins with functions in m6A writing interact with HAKAI. Nature Communications, 13(1), 1127.

Bredeson, J.V., Lyons, J.B., Oniyinde, I.O., Okereke, N.R., Kolade, 0., Nnabue, I., Nwadili, C.O., Hřibová,E., parker, M.T.,Nwogha,J., Shu, S., Carlson, J., Kariba, R., Muthemba, S., knop, K., Barton, G.J., Sherwood, A.V., Lopez-Montes, A., Asiedu, R., Jamnadass, R., Muchugi, A., Goodstein, D., Egesi, C.N., Featherston, J., Asfaw, A., Simpson, G.G., Doležel, J., Hendre, P.S., Van Deynze, A., Kumar, P.L., Obidiegwu, J.E., Bhattacharjee, R., Rokhsar, D.S. (2022). Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nature Communications, 13(1), 2001.

Parker, M. T., Barton, G. J., & Simpson, G. G. (2021). Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads. In bioRxiv (p. 2021.06.15.448494).

Parker, M. T., Knop, K., Zacharaki, V., Sherwood, A. V., Tomé, D., Yu, X., Martin, P. G., Beynon, J., Michaels, S. D., Barton, G. J., & Simpson, G. G. (2021). Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife, 10, e65537.

Parker, M. T., Knop, K., Barton, G. J., & Simpson, G. G. (2021). 2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing. In Genome Biology 22, 72.

Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., Mackinnon, K., Gould, P. D., Hall, A. J., Barton, G. J., & Simpson, G. G. (2020). Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife, 9, e49658.

The image shows a phylogenetic tree of 227 Saccharomycotina species and an outgroup of 13 species with well-annotated genomes, including the human genome. The overall tree and the branches of relatedness between species make an almost complete circle. Rings around the outside of the tree first give the species name.

Figure 1: We used inter-species association mapping to show that the evolution of 5’ splice site sequence preference is linked to the splicing factor SNRNP27K and the enzyme METTL16, which methylates U6snRNA. From Parker et al., 2023.

View full research profile and publications


I teach Genetics and Advanced Plant Science. My lab hosts final year Honours students carrying out their research projects, and Masters and Erasmus students from overseas.


Research interests

RNA and Development


Award Year
Fellow of the Royal Society of Biology 2015