Investigating how plants use RNA to cope with stress

The diversity of RNA structure is wide and varied, from hairpins and bulges through to triplex and quadruplexes. These structures are able to control numerous biological functions from sensing messenger compounds to dictating whether genes are switched on or off. This project will focus in particular on G-quadruplexes, four-stranded RNA structures which are formed from sequences which contain a lot of the base guanine. This project will aim to reveal some of the RNA-based mechanisms which alter gene regulation in plants in response to stress (for example during periods of drought).

This PhD project will involve using biophysical and molecular biology techniques to determine the type of structures which the RNA is able to fold into, how they change in response to the environment and what happens to the biology when they form. The project will be highly interdisciplinary and will involve training in a wide range of techniques, from biophysical and physiological characterisation to in vivo testing in plants. Led by Prof. Yiliang Ding and Prof. Antony Dodd at the John Innes Centre along with Prof. Zoë Waller in the University College London, the successful applicant will enjoy the benefits of working in both a University environment and research institute.

The student will have, or expect to obtain a first-class, 2(i) or equivalent Honours degree in Biology, Chemistry, Biochemistry, Pharmacy or a related area.
Informal enquiries are welcomed; for further information please contact Prof Yiliang Ding (Yiliang.Ding@jic.ac.uk).

References

Yu H, Qi Y, Yang B, Yang X, Ding Y. G4Atlas: a comprehensive transcriptome-wide G-quadruplex database. Nucleic Acids Res. 2023;51(D1):D126-D134.

Yang X, Yu H, Duncan S, Zhang Y, Cheema J, Liu H, Miller JB, Zhang J, Kwok CK, Zhang H, Ding Y. RNA G-quadruplex structure contributes to cold adaptation in plants. Nat Commun. 2022;13(1).

Yang M, Zhu P, Cheema J, Bloomer R, Mikulski P, Liu Q, Zhang Y, Dean C, Ding Y. In vivo single-molecule analysis reveals COOLAIR RNA structural diversity. Nature. 2022;609(7926):394-399.

Yang X, Cheema J, Zhang Y, Deng H, Duncan S, Umar MI, Zhao J, Liu Q, Cao X, Kwok CK, Ding Y. RNA G-quadruplex structures exist and function in vivo in plants. Genome Biol. 2020;21(1):226.

Paajanen, P., Lane de Barros Dantas, L. & Dodd, A. N. Layers of crosstalk between circadian regulation and environmental signalling in plants. Curr Biol 31, R399-R413, (2021).