Professor Gordon Simpson

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 https://doi.org/10.1101/2023.05.04.539401.

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. https://elifesciences.org/articles/78808

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. https://doi.org/10.1038/s41467-022-28753-3

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. https://doi.org/10.1038/s41467-022-29114-w

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). https://doi.org/10.1101/2021.06.15.448494

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. https://doi.org/10.7554/eLife.65537

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. https://doi.org/10.1186/s13059-021-02296-0

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. https://doi.org/10.7554/eLife.49658

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.