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John Brown

Staff picture: John Brown
Head of University of Dundee Division of Plant Sciences
Cell and Molecular Sciences
Head of University of Dundee Division of Plant Sciences
John.Brown@hutton.ac.uk
+44 (0)344 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

 

Employment History

  • April 2011-present: Professor of Molecular Plant Science, Division of Plant Sciences, College of Life Sciences, University of Dundee (at The James Hutton Institute)
  • October 2007-April 2011: Professor of Molecular Plant Science, Division of Plant Sciences, College of Life Sciences, University of Dundee (at SCRI)
  • 1990-2007: Group Leader and various positions of responsibility, SCRI
  • 1988-1990: Lecturer, Biological Sciences, University of Dundee
  • 1979-1987: Postdocs in USA and Germany
  • 1976-1979: PhD University of Cambridge/Plant Breeding Institute
  • 1971-1975: BSc (Hons) University of Edinburgh

Current research interests

The regulation of gene expression at the post-transcriptional level is important in many aspects of plant growth and development, and plant response to pathogens and the environment in which they grow. Knowledge of the complexity of how genes are expressed in different processes will provide understanding of the genetic basis of important phenotypic traits.

The importance of post-transcriptional gene regulation is growing exponentially. Clearly gene expression control is complex and dynamic, involving different RNA and RNP species and interactions among different RNA processing pathways. In addition, the structure and organisation of the nucleus into different regions and compartments is essential for the dynamic assembly and transport of complexes to drive such interactions. Currently, our main interests in gene expression are in alternative splicing, the functions of the plant nucleolus in mRNA biogenesis and the gene organisation and function of small nucleolar RNAs (snoRNAs).

We have studied aspects of plant intron splicing for many years demonstrating exon definition and the roles of branchpoints, polypyrimidine tracts and UA-rich signals. We are using our expertise on splicing analysis to study mechanisms and consequences of alternative splicing, and are establishing systems to study multiple splicing events simultaneously. In particular, we are interested in how alternative splicing affects gene expression during development and in response to stress, and how it is controlled by a range of trans-acting factors.

We identified exon junction complex proteins in a proteomic analysis of plant nucleoli (with Professor Peter Shaw, John Innes Centre). We have found mRNAs to be present in the nucleolus and an enrichment of aberrant mRNAs. We are currently examining what these observations mean in terms of the function of the nucleolus in mRNA biogenesis and the link to alternative splicing and mRNA turnover.

SnoRNAs are one of the best studied non-coding RNA groups. The majority of plant snoRNA genes are organized in gene clusters and expressed as polycistronic precursor snoRNAs (pre-snoRNAs). We are examining “orphan” snoRNAs and the effects which these may have on mRNA expression and stability.

Key Collaborators

  • Peter Shaw (John Innes Centre, UK)
  • Andrea Barta (Medical University of Vienna, Austria)
  • Artur Jarmolowski (Adam Mickiewicz University, Poznan, Poland)

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, Chapter 17, pp269-281.
  • 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.
  • Barta, A.; Marquez, Y.; Brown, J.W.S., (2012) Challenges in plant alternative splicing., In: Stamm, S., Smith, C.W.J. & Lührmann, R. (eds.). Alternative pre-mRNA Splicing: Theory and Protocols. Wiley-Blackwell, Weinheim, Germany, 79-91.
  • 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.
  • Brown, J.W.S.; Shaw, P.J., (2008) The role of the plant nucleolus in pre-mRNA processing., In: Reddy, A.S.N. & Golovkin, M. (eds.). Nuclear Pre-mRNA Processing in Plants. Springer, New York, Chapter 326, 291-311.
  • Waugh, R.; Brown, J.W.S., (1991) Plant gene structure and expression., In: Grierson, D. (ed.). Plant Genetic Engineering. Plant Biotechnology Series. Blackie Scientific, pp1-36.

  • 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.
  • Kim, S.; Ryabov, E.V.; Gillespie, T.; MacFarlane, S.A.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E., (2007) Nuclear voyage of a plant virus protein., Annual Report of the Scottish Crop Research Institute for 2006, pp22-23.
  • Machray, G.C.; Brown, J.W.S.; Oparka, K.J.; Torrance, L., (2002) Mechanisms and Processes., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp101-104.
  • 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.
  • Machray, G.C.; Hedley, P.E.; Davidson, D.; Ibrahim, A.F.M.; Watters, J.A.; Brown, J.W.S., (1999) Promoting plant promoters., Annual Report of the Scottish Crop Research Institute for 1998/99, pp82-85.
  • 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.

Scientific posters/conferences

AttachmentSize
File Comparing Carbon Fixation Between Two Species Of The Marine Diatom Thalassiosira 98.13 KB
File European Alternative Splicing Network 854.82 KB
File Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli 267.47 KB
File The use of anti-nematode and anti-feeding site factors to obtain resistance against potato cyst nematodes (PCN) 169.51 KB
File Silencing Genes Involved in Post-transcriptional Gene Expression 171.83 KB
File Arabidopsis Databases at the Scottish Crop Research Institute (SCRI) 889.25 KB
File Plant Exon Junction Complex (EJC) proteins 610.32 KB
File Stacking of novel anti-nematode and anti-feeding site factors to obtain resistance against plant parasitic nematodes 183.05 KB
File Plant Exon and Intron Splicing Enhancers 280.32 KB
File The Plant Genomics Database Infrastructure at the Scottish Crop Research Institute 213.29 KB
File The plant nucleolus functions in mRNA export and NMD 326.58 KB
File Altered Splicing of a Mini-exon by Over-expression of Arabidopsis PTB-like Proteins 290.23 KB
File An RT-PCR Panel to Monitor Changes in Alternative Splicing in Multiple Genes 191.89 KB
File The Plant Nucleolus: functions in mRNA export or NMD? 894.31 KB
File Revealing the past: New insights into plant evolution using a novel snoRNA marker-system 197.39 KB
File Regulation of gene expression by alternative splicing and nonsense-mediated decay 283.81 KB
File European Alternative Splicing Network of Excellence (EURASNET) 353.89 KB
File A plant virus movement protein forms ringlike complexes with the major nucleolar protein Fibrillarin in vitro 229.91 KB
File Alternative splicing and NMD in Arabidopsis 180.55 KB
File Arabidopsis PTB-like 1 (AtPTBL1) negatively regulates splicing inclusion of a plant mini-exon 339.89 KB
File Intron retention in Arabidopsis mRNA transcripts 122.3 KB
File Alternative splicing and nonsense mediated decay in Arabidopsis 318.35 KB
File Alternative splicing and nonsense-mediated decay controls expression of important regulatory genes in Arabidopsis
217.73 KB
File Expression and Alternative Splicing in Circadian Clock Genes Respond to Temperature Changes
220.6 KB

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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.