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Craig Simpson

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

The James Hutton Institute
Invergowrie
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.

Bibliography

  • 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, 269-281
  • 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, 121-144
  • 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, 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. Cham: Springer, Chapter 14, pp 199-212
  • 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.

  • Simpson, C.G.; Fuller, J.; Lewandowska, D.; Davidson, D.; Brown, J.W.S. (2011) Alternative splicing in response to abiotic stress., Annual Report of the Scottish Crop Research Institute for 2010, pp16-17.
  • Simpson, C.G.; Thow, G.; Clark, G.P.; Jennings, N.; Brown, J.W.S. (2002) Detailed analysis of two intron splicing signals., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp105-107.
  • Brown, J.W.S.; Clark, G.P.; Thow, G.; Simpson, C.G. (2001) SnoRNA gene clusters., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp87-88.
  • Simpson, C.G.; Clark, G.P.; Watters, J.; Brown, J.W.S. (2000) How small is an exon - does size matter?., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp111-113.
  • Hamilton, J.I.; Simpson, C.G.; Clark, G.P.; McQuade, C.; Lyon, J.M.; Watters, J.A.; Brown, J.W.S. (1999) Plant genes for the spliceosomal protein, PRP8., Annual Report of the Scottish Crop Research Institute for 1998/99, pp80-81.
  • Simpson, C.G.; Hedley, P.E.; McQuade, C.M.; Lyon, J.M.; Clark, G.P.; Machray, G.C.; Brown, J.W.S. (1998) Splicing regulation of a potato invertase mini-exon., Annual Report of the Scottish Crop Research Institute for 1997/98, pp71-73.
  • Machray, G.C.; Hedley, P.E.; Simpson, C.G.; Waugh, R.; Brown, J.W.S. (1994) PCR methods for the analysis of expression from plant multigene families., Annual Report of the Scottish Crop Research Institute fro 1993, p116.

  • Cullen, D.W.; McCallum, S.; Paterson, A.; Hedley, P.E.; Simpson, C.G.; Milne L.; Graham, J. (2013) Fruit quality in red raspberry., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013.
  • McCallum, S.; Cullen, D.W.; Hedley, P.; Simpson, C.; Hancock, R.D.; Milne, L.; Hackett, C.A.; Graham J. (2013) Control of fruit quality traits in red raspberry, a review from James Hutton Institute., Fruits and Roots: A Celebration and Forward look, East Malling Research, Kent, 6-7 November 2013.
  • Cullen, D.W.; Woodhead, M.; Ross, H.A.; Simpson, C.G.; Hallett, P.D.; Hackett, C.A.; Graham, J. (2012) Developing breeding and selection tools to reduce spoilage of soft fruit and wastage in the supply chain., Bulrush Horticulture Ltd and Scottish Society for Crop Research Information Day and Winter Meeting, Dundee, 15 February 2012.
  • Cullen, D.W.; Woodhead, M.; Ross, H.A.; Simpson, C.G.; Hallett, P.D.; Hackett, C.A.; Graham, J. (2012) Developing breeding and selection tools to reduce spoilage of soft fruit and wastage in the supply chain., Autumn Growers' Meeting and Technical Conference, Sutton Heights, Shropshire, 14-15 November 2012.
  • Cullen, D.W.; Woodhead, M.; Ross, H.A.; Simpson, C.G.; Hackett, C.A.; Graham, J. (2012) Developing breeding and selection tools to reduce spoilage of soft fruit and wastage in the supply chain., Molecular Mapping and Marker Assisted Selection, Vienna, Austria, 8-11 February 2012.
  • James, A.B.; Lewandowska, D.; Simpson, C.G.; Brown, J.W.S.; Nimmo, H.G. (2011) Polypyrimidine tract binding proteins (PTBs) - a possible role in the alternative splicing of Arabidopsis clock genes during responses to temperature., Annual Main Meeting of Society for Experimental Biology, Glasgow, 1-4 July 2011.
  • Brown, J.W.S.; Simpson, C.G.; Lewandowska, D.; Clark, G.; Fuller, J.; Kim, S.; Pendle, A.; Shaw, P.J.; Koroleva, O. (2009) The plant Nucleolus, mRNA and nonsense-mediated decay., Eurasnet UK RNA Splicing Workshop, Lake District, 23-25 January 2009, 10.
  • Maranova, M.; Kalyna, M.; Simpson, C.G.; Brown, J.W.S.; Barta, A. (2008) Identifying RNA targets of the Arabidopsis thalians splicing factor atRSp31., RNA 2008, 13th Annual Meeting of the RNA Society. Berlin, Germany, 28 July - 3 August 2008.
  • Raczynska, D.; Ciesiolka, A.; Szewc, L.; Simpson, C.G.; Szweykowska-Kulinska, Z.; Brown, J.W.S.; Jarmolowski, A. (2008) The involvement of the nuclear cap binding protein complex in alternative splicing in Arabidopsis thaliana., 1st International EURASNET Conference on Alternative Splicing, Krakow, Poland, 21-23 May 2008.
  • Simpson, C.G.; Lewandowska, D.; Fuller, J.; Maronova, M.; Kalyna, M.; Davidson, D.; McNicol, J.W.; Raczynska, D.; Jarmolowski, A.; Barta, A.; Brown, J.W.S. (2008) Monitoring alternative splicing in multiple plant genes., 1st International EURASNET Conference on Alternative Splicing, Krakow, Poland, 21-23 May 2008.
  • Simpson, C.G.; Lewandowska, D.; Fuller, J.; Kalyna, M.; Davidson, D.; McNicol, J.W.; Barta, A.; Brown, J.W.S. (2008) NMD is involved in the turnover of PTC-containing alternatively spliced transcripts in Arabidopsis., 1st International EURASNET Conference on Alternative Splicing, Krakow, Poland, 21-23 May 2008.
  • Simpson, C.G.; Lewandowska, D.; Fuller, J.; Maronova, M.; Kalyna, M.; Davidson, D.; McNicol, J.W.; Raczynska, D.; Jarmolowski, A.; Barta, A.; Brown, J.W.S. (2008) Alternative splicing in plants., UK RNA Processing Meeting, Lake District, January 2008.
  • Simpson, C.G.; Fuller, J.; Fusekova, M.; Davidson, D.; McNicol, J.W.; Barta, A.; Brown, J.W.S. (2008) Monitoring changes in alternative pre-mRNA splicing in multiple gene transcripts., Scottish Plant Biology Meeting. SCRI and University of Dundee, Invergowrie, Dundee, 11 January 2008.
  • Simpson, C.G.; Chapman, S.N.; Clark, G.; Liney, M.; Brown, J.W.S. (2007) Over-expression of Arabidopsis PTB-like proteins cause changes in splicing of a mini-exon., 6th Post-Transcriptional Regulation of Plant Gene Expression, Carry-le-Rouet, France, 10-13 May 2007.
  • Simpson, C.G.; Lewandowska, D.; Fuller, J.; Maronova, M.; Kalyna, M.; Davidson, D.; McNicol, J.W.; Raczynska, D.; Jarmolowski, A.; Barta, A.; Brown, J.W.S. (2007) An RT-PCR panel to monitor changes in alternative splicing in multiple genes., 6th Post-Transcriptional Regulation of Plant Gene Expression, Carry-le-Rouet, France, 10-13 May 2007.
  • Simpson, C.G.; Fuller, J.; Fusekova, M.; Davidson, D.; McNicol, J.W.; Barta, A.; Brown, J.W.S. (2007) Monitoring changes in alternative pre-mRNA splicing in multiple gene transcripts., Plant Science Scotland - Plant Biology, University of Glasgow, 5 January 2007.
  • Simpson, C.G.; Chapman, S.N.; Clark, G.; Liney, M.; Brown, J.W.S. (2007) Altered splicing of a mini-exon by over-expression of Arabidopsis PTB-like proteins., EURASNET 2nd Annual Meeting, Ilse de Bandor, France, 14-18 April 2007.
  • Simpson, C.G.; Fuller, J.; Maronova, M.; Kalyna, M.; Davidson, D.; McNicol, J.W.; Jarmolowski, A.; Barta, A.; Brown, J.W.S. (2007) Plant alternative splicing RT-PCR panel., EURASNET 2nd Annual Meeting, Ile de Bender, France, 14-18 April 2007.
  • Simpson, C.G.; Chapman, S.N.; Clark, G.; Liney, M.; Brown, J.W.S. (2007) Over-expression of plant RNA binding proteins induces alternative mini-exon splicing., UK RNA Processing Meeting, Lake District, 19-21January 2007.
  • Simpson, C.G.; Leader, D.J.; Clark, G.P.; Lopez, M.M.; Brown, J.W.S. (2001) SnoRNA genes from Arabidopsis., 6th Annual Meeting of the RNA Society, Banff, Canada, 29 May - 3 June 2001.
  • Simpson, C.G.; Thow, G.; Clark, G.P.; Watters, J.A.; Jennings, N.; Brown, J.W.S. (2001) Detailed analysis of a plant branchpoint and polypyrimidine tract., 6th Annual Meeting of the RNA Society, Banff, Canada, 29 May - 3 June 2001, 493.
  • Simpson, C.G.; Thow, G.; Clark, G.P.; Jennings, N.; Brown, J.W.S. (2001) Detailed analysis of a plant branchpoint and polypyrimidine tract in splicing of a mini-exon., Scottish Plant Molecular and Cell Biology Forum, Dundee, January 2001.
  • Blanco, P.; Thow, G.; Simpson, C.G.; Villa, T.G.; Williamson, B. (2000) Expression of an endo-polygalacturonase from Saccharomyces cerevisiae in Pichia pastoris., 10th International Symposium on Yeasts, Papendal, The Netherlands, 27 August - 1 September 2000.
  • Simpson, C.G.; Clark, G.P.; McQuade, C.M.; Watters, J.A.; Hedley, P.E.; Machray, G.C.; Brown, J.W.S. (2000) Splicing of a mini-exon from potato invertase pre-mRNAs., Scottish Plant Molecular and Cell Biology Forum, St Andrews University, 28 January 2000.
  • Blanco, P.; Thow, G.; Simpson, C.G.; Villa, T.G.; Sieiro, C.; Williamson, B. (2000) Estudio de una endopoligalacturonasa de Saccharomyces cerevisiae mediante mutagÚnesis dirigida., 5th National Congress of Mycology, Caceres, Spain,20-23 September 2000.
  • Brown, J.W.S.; Simpson, C.G.; Hedley, P.E.; McQuade, C.M.; Lyon, J.M.; Watters, J.A.; Machray, G.C. (1999) Exon bridging interactions in plant pre-mRNA splicing., Proceedings XVI International Botanical Congress, St Louis, Missouri, USA, 26 July 1999.
  • Thow, G.; Simpson, C.G.; Williamson, B. (1998) Heterologous expression of raspberry PGIP in Escherichia coli to investigate the binding and inhibition of fungal endo-PG., Proceedings of the International Congress of Plant Pathology, Edinburgh, 9-16 August 1998, No. 5.3.24.
  • Iannetta, P.P.M.; James, E.K.; Thow, G.; Minchin, F.R.; Simpson, C.G.; Sprent, J.I.; Williamson, B. (1998) Immunolocalisation of polygalacturonase-inhibiting protein (PGIP) in white lupin., Proceedings of 8th Scottish Cell Wall Group Meeting, Dundee, 8-9 April 1998, 6.

  • Spensley, M.; Simpson, C.G.; Brown, J.W.S. (2013) Conservation of alternative exons in plants., Post-Transcriptional Gene Regulation in Plants, Providence, Rhode Island, USA, 25-26 July 2013 (Abstract).
  • Sanchez, S.E.; Legris, M.; Petrillo, E.; Seymour, D.K.; Mancini, E.; Chernomoretz, A.; Weigel, D.; Brown, J.W.S.; Simpson, C.G.; Kornbilhtt, A.R.; Yanovsky, M.J. (2013) PICin, an SnRNP assembly related protein, plays a role in the regulation of alternative splicing, development and stress responses in Arbidopsis., Post-Transcriptional Gene Regulation in Plants, Providence, Rhode Island, USA, 25-26 July 2013 (Abstract).
  • Cullen, D.W.; McCallum, S.; Paterson, A.; Hedley, P.E.; Simpson, C.G.; Milne L.; Graham, J. (2013) Fruit quality in red raspberry (W308)., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, p163.
  • Carvalho, R.; Carvalho S.; Simpson, C.G.; Brown, J.W.S.; Baena-Gonzalez, E.; Duque, P. (2013) Stress responses mediated by the plant-specific SR45 and SCL30a splicing factors are ABA-dependent., Post-Transcriptional Gene Regulation in Plants. Providence, Rhode Island, USA, 25-26 July 2013 (Abstract).
  • Bardou, F.; Ariel, F.; Sorin C.; Christ, A.; Simpson, C.G.; Brown, J.W.S.; Lelandais, C.; Hartmann, C.; Crespi, M. (2013) Modulation of alternative splicing by long non-coding RNAs., Post-Transcriptional Gene Regulation in Plants, Providence, Rhode Island, USA, 25-26 July 2013 (Abstract).
  • Simpson, C.G.; Kalyna, M.; Shaw, P.; McNicol, J.W.; Marquez, Y.; Barta, A.; Brown, J.W.S. (2012) Arabidopsis ecotype alternative splicing variants., ICAR RNA Satellite Meeting, Vienna, Austria, 3-7 July 2012 (Poster).
  • Simpson, C.G.; Kalyna, M.; Fuller, J.; Shaw, P.; McNicol, J.; Marquez, Y.; Barta, A.; Brown, J.W.S. (2012) Arabidopsis ecotype alternative splicing variants., Plant RNA Workshop, Vienna, Austria, 8-9 July 2012 (Poster).
  • Marquez, Y.; Brown, J.W.S.; Ayatollaho, Z.; Simpson, C.G.; Kalyna, M.; Barta, A. (2012) Unravelling the alternative splicing landscape in Arabidopsis using RNA-seq., First Post-EURASNET Symposium, Trieste, Italy, 24-27 March 2012 (Poster).
  • Kalyna, M.; Maronova, M.; Fuchs, A.; Ayatollaho, Z.; Simpson, C.G.; Brown, J.W.S.; Barta, A. (2012) Plant specific Ser/Arg-rich splicing factor RS31 acts as a regulator of DNA repair and stress response., Plant RNA Workshop, Vienna, Austria, 8-9 July 2012 (Poster).
  • Cullen, D.W.; Woodhead, M.; Ross, H.A.; Simpson, C.G.; Hallett, P.D.; Hackett, C.A.; Graham, J. (2012) Developing breeding and selection tools to reduce spoilage of soft fruit and wastage in the supply chain., Molecular Mapping & Marker Assisted Selection Conference. Vienna, Austria, 8-11 February 2012, N10.
  • Carvalho, R.; Simpson, C.G.; Barbosa, I.; Brown, J.W.S.; Baena-Gonzalez B.; Dugue, P. (2012) The SR45 plant-specific splicing factor, a negative regulator of sugar signalling modulates SNRK1.1 levels and targets alternative splicing of several genes in Arabidopsis., Plant RNA Workshop, Vienna, Austria, 8-9 July 2012 (Poster).
  • Simpson, C.G.; Kalyna, M.; Syed, N.H.; Marquez, Y.; Barta, A.; Brown, J.W.S. (2011) Alternative splicing and nonsense-mediated decay controls expression of important regulatory genes in Arabiodpsis., RNA 2011, Kyoto, Japan, 14-18 June 2011.
  • Simpson, C.G.; Brown, J.W.S.; Barta, A.; McNicol, J.W.; Maronova, M.; Kalyna, M.; Kusenda, B.; Milne, L. (2011) SR-protein specific changes in Arabidopsis alternative splicing., Annual Main Meeting of Society for Experimental Biology, Glasgow, 1-4 July 2011. (Poster)
  • Brown, J.W.S.; Kalyna, M.; Simpson, C.G.; Marquez, Y.; Barta, A. (2011) Alternative splicing and nonsense-mediated decay controls expression controls of important regulatory genes in Arabidopsis., EURASNET Conference on Alternative Splicing, Granada, Spain, 28 February -3 March 2011. Poster
  • Simpson, C.G.; Kalyna, M.; Lewandowska, D.; Kusenda, B.; Fuller, J.; Milne, L.; McNicol, J.W.; Clark, G.; Barta, A.; Brown, J.W.S. (2010) Alternative splicing and NMD in Arabidopsis., EURASNET Annual Meeting 2010, Lisbon, Portugal, 1-4 March 2010 (Poster).
  • Simpson, C.G.; Kalyna, M.; Lewandowska, D.; Kusenda, B.; Fuller, J.; Milne, L.; McNicol, J.W.; Barta, A.; Brown, J.W.S. (2010) Alternative splicing and nonsense mediated decay in Arabidopsis., Biochemical Society: Post-Transcriptional Control: mRNA Translation, Localisation and Turnover, Edinburgh, 8-10 June 2010. 227 (Poster).
  • Simpson, C.G.; Kalyna, M.; Lewandowska, D.; Kusenda, B.; Fuller, J.; Milne, L.; McNicol, J.W.; Clark, G.; Barta, A.; Brown, J.W.S. (2010) Alternative splicing and NMD in Arabidopsis., RNA 2010, Seattle, WA, USA, 22-26 June 2010. 193 (Poster).
  • Kalyna, M.; Bannikova, O.; Maronova, M.; Simpson, C.G.; Brown, J.W.S.; Barta, A. (2010) RNA targets of plant-specific SR-proteins and their role in stress response., RNA 2010, Seattle, WA, USA, 22-26 June 2010 (Poster).
  • Sanchez, S.E.; Petrillo, E.; Beckwith, E.J.; Zhang, X.; Hernando, C.E.; Rugnone, M.L.; Simpson, C.G.; Brown, J.W.S.; Cerdan, P.D.; Borevitz, J.O.; Ceriani, M.F.; Mas, P.; Kombilhtt, A.R.; Yanovsky, M.J. (2010) A role for AtPRMTS in the Arabidopsis circadian network., Plant Biology 2010, Montreal, Canada, 31 July - 4 August 2010. Abstract P08123 (Poster).
  • Raczynska, K.D.; Konieczna, M.; Ciesiolka, A.; Lewandowska, D.; Simpson, C.G.; Karowski, W.; Szweykowska-Kulinska, Z.; Brown, J.W.S.; Jarmolowski, A. (2010) Regulation of alternative splicing in Arabidopsis thaliana., SEB Annual Main Meeting 2010, Prague, Czech Republic, 30 June - 3 July 2010 (Poster).

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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.