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Craig Simpson

Staff picture: Craig Simpson
Cell and Molecular Sciences
Cell and Molecular Sciences
Senior Postdoctoral Scientist
+44 (0)344 928 5428 (*)

The James Hutton Institute
Dundee DD2 5DA
Scotland UK


Craig is a plant molecular biologist and experimental scientist who is interested in environmental gene expression responses in barley. He is utilising genome-wide RNA-seq transcript abundance datasets to identify important barley genes and gene pathways in phenotypically divergent barley tissues or barley grown under variable environmental conditions. He has recently focused on the short-term cold acclimation gene expression response in spring barley types and the importance of alternative expressed transcripts.


  • April 2011-present: Postdoctoral research scientist, The James Hutton Institute
  • 2007-present: Postgraduate Liaison Officer at the Institute
  • 1991–April 2011: Postdoctoral research scientist, SCRI
  • 1988–1991: Research Assistant, University of Dundee, Dundee
  • 1986–1988: Scientific Officer, Plant Breeding Institute, Cambridge
  • PhD Dundee University
  • BSc (Hons) University of St Andrews

Current research interests

He is interested in how plant genes express themselves in response to environmental and developmental changes.

  • Gene expression involves a number of highly co-ordinated and actively regulated steps. Splicing is one important step in this process. Alternative splicing, where many different mRNAs can be derived from a single gene, increases cell protein complexity and function. We have established a system that allows us to measure changes in alternative splicing of hundreds of genes simultaneously. We are using this system to monitor changes in alternative splicing during tissue, developmental and environmental responses. We are also measuring the effect of changes in splicing factor concentrations by measuring changes of alternative splicing in knockout, mutant or over-expressing plant lines.
  • Splice site selection is generally regulated through the interaction of protein splicing factors with RNA sequence elements that promote or inhibit the selection of associated splice sites. We are studying the role of Polypyrimidine Tract Binding – like proteins (PTB-L) in plant splicing and their ability to influence plant splice site choice.
  • The expression of a number of RNA binding proteins and their cellular location are influenced by the onset of stresses, such as temperature for example. We are interested in a number of RNA binding domain containing proteins that show increased expression in response to stress.

Past research

Along with other groups we have established splicing sequences required for efficient and accurate plant pre-mRNA splicing.


  • Simpson, C.G.; Fuller, J.; Flores, J.; Mayer, C-D.; Calixto, C.P.G.; Milne, L.; Hedley, P.E.; Booth, C.; Waugh, R.; Brown, J.W.S. (2019) High resolution RT-PCR analysis of alternative barley transcripts., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 17, pp269-281.
  • McCallum, S.; Simpson, C.; Graham, J. (2018) QTL mapping and marker assisted breeding in Rubus spp., In: Graham, J. & Brennan, R. (eds.). Raspberry: Breeding, Challenges and Advances. Springer International Publishing, Cham, Chapter 8, pp121-144.
  • Simpson, C.G.; Barrero, R.A.; Bayer, M.; Flavell, A.; Rapazote-Flores, P.; Bellgard, M.I.; Hedley, P.E.; Zhang, R.; Waugh, R. (2018) The expressed portion of the barley genome., In: Stein, N. & Muehlbauer, G. (eds.). The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, Chapter 7, 789-107.
  • Graham, J.; Simpson, C. (2018) Developmental transitions to fruiting in red raspberry., In: Hytonen, T., Graham, J., Harrison, R. (eds.). The Genomes of Rosaceous Berries and their Wild Relatives. (Compendium of Plant Genomes) Springer, Chapter 14, pp199-212.
  • Simpson, C.G.; Fuller, J.; Calixto, C.; McNicol, J.; Booth, C.; Brown, J. W.S.; Staiger, D. (2016) Monitoring alternative splicing changes in Arabidopsis circadian clock genes., In: Duque, P. (eds.). Environmental Responses in Plants: Methods and Protocols. Methods in Molecular Biology Volume 1398. Humana Press, New York, pp119-132.
  • Simpson, C.G.; Syed, N.H.; Manthri, S.; Fuller, J.D.; Maronova, M.; Kusenda, B.; Kalyna, M.; Barta, A.; Brown, J.W.S. (2012) Monitoring changes in plant alternative splicing events., In: Stamm, S., Smith, C.W.J. & Lührmann, R. (eds.). Alternative pre-mRNA Splicing: Theory and Protocols. Wiley-Blackwell, Weinheim, Germany, 249-259.
  • Simpson, C.G.; Liney, M.; Davidson, D.; Lewandowska, D.; Kalyna, M.; Chapman, S.N.; Barta, A.; Brown, J.W.S. (2012) In vivo analysis of plant splicing., In: Stamm, S., Smith, C.J.W. & Luhrmann, R. (eds.). Alternative pre-mRNA Splicing: Theory and Protocols. Wiley-Blackwell, Weinheim, Germany, Chapter 42.
  • Simpson, C.G.; Brown, J.W.S. (2008) U-12 dependent intron splicing in plants., In: Nuclear Pre-mRNA Processing in Plants (eds. A.S. Reddy and M. Golovkin). Springer, New York, pp61-82.

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.