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John Brown

Staff picture: John Brown
University of Dundee Division of Plant Sciences
University of Dundee Division of Plant 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.

  • Taliansky, M.E.; Shaw, J.; Kim, S.; Ryabov, E.; Kalinina, N.O.; MacFarlane, S.A.; Brown, J.W.S. (2011) Involvement of the cell nucleus in plant virus systemic infections., Society for General Microbiology Spring Conference, Harrogate, 11-14 April 2011. Session: Seeing the cell through the Eyes of the Virus.
  • 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.
  • Shaw, P.; Brown, J.W.S. (2010) Subnuclear structures in plants., Subnuclear Structures and Disease, Wellcome Trust Conference, Cambridge, 27-30 July 2010.
  • Shaw, J.; Canetta, E.; Kim, S.; Kalinina, N.O.; Adya, A.K.; Brown, J.W.S.; Taliansky, M.E. (2009) A plant virus movement protein forms ringlike complexes with major nucleolar protein, fibrillarrin in vitro., Association of Applied Biologists. Advances in Plant Virology, Harrogate, 1-3 April 2009.
  • 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.
  • Koroleva, O.; Calder, G.; Pendle, A.; Kim, S.; Lewandowska, D.; Brown, J.W.S.; Shaw, P.J. (2008) Dynamic behaviour of the eIF4AIII, putative core protein of Exon Junction Complex: Fast relocation to nucleolus and splicing speckles under stress., Annual Meeting of the Society for Experimental Biology, Marseille, France, 6-10 July 2008. Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology 150, S146.
  • Brown, J.W.S.; Lewandowska, D.; Kim, S.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2008) The Arabidopsis nucleolus accumulated aberrant mRNAs and UPF2 and UPF3 suggesting a role in nonsense-mediated decay., UK RNA Processing Meeting, Lake District, 18-20 January 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.
  • Brown, J.W.S.; Kim, S.; Koroleva, O.; Pendle, A.; Lewandowska, D.; McKeown, P.; Shaw, P.J. (2007) The plant nucleolus functions in mRNA export and NMD., RNA Society Meeting. Madison, USA, 29 May - 2 June 2007.
  • Brown, J.W.S.; Kim, S.; Koroleva, O.; Pendle, A.; Lewandowska, D.; McKeown, P.; Shaw, P.J. (2007) The plant nucleolus functions in mRNA export and NMD., 6th Post-Transcriptional Regulation of Plant Gene Expression. Carry-le-Rouet, France, 10-13 May 2007.
  • Brown, J.W.S.; Kim, S.; Pendle, A.; Koroleva, O.; Lewandowska, D.; McKeown, P.; Shaw, P.J. (2007) Proteomic and RNomic analysis of Arabidopsis nucleoli indicate novel functions for the nucleolus., Keystone Meeting: Plant Cell Biology, Idaho, USA, 23-28 March 2007.
  • Shaw, P.J.; Pendle, A.; Koroleva, O.; Lewandowska, D.; Kim, S.; Brown, J.W.S. (2007) Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli., Joint Bioinformatics and E-science, Proteomics and Cell Function Grantholders Workshop. BBSRC, Carden Park, Cheshire, 8-10 January 2007.
  • Kim, S.; Pendle, A.; Koroleva, O.; Lewandowska, D.; Shaw, P.J.; Brown, J.W.S. (2007) Proteomic and RNomic analyses of Arabidopsis nucleoli indicate novel functions for the nucleolus., Plant Science Scotland - Plant Biology, University of Glasgow, 5 January 2007.
  • Kim, S.; MacFarlane, S.A.; Kalinina, N.; Rakitina, D.V.; Ryabov, E.; Gillespie, T.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E. (2007) Interaction between a plant virus-encoded protein and the major nucleolar protein fibrillarin, is required for virus systemic infection., AAB Advances in Virology, University of Greenwich, 11-12 September 2007.
  • Taliansky, M.E.; Kim, S.; Ryabov, E.V.; Kalinina, N.; Rakitina, D.V.; Gillespie, T.; MacFarlane, S.A.; Brown, J.W.S. (2006) Involvement of the nucleolus in plant virus systemic infection., EMBO Workshop 'The Nucleolus: New Perspectives'. York, 27-30 March 2006.
  • Brown, J.W.S.; Kim, S.; Lewandowska, D.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2006) Arabidopsis nucleoli are enriched in aberrantly spliced mRNAs., EMBO Workshop - The Nucleolus: New perspectives, York, 27-30 March 2006.
  • Brown, J.W.S.; Lewandowska, D.; Kim, S.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2006) Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli., UK RNA Processing Meeting. Lake District, 20-22 January 2006.
  • Brown, J.W.S.; Lewandowska, D.; Kim, S.; Pendle, A.; Koroleva, O.; Shaw, P.J. (2006) Proteomic and RNomic analysis of the nucleolus: novel functions in mRNA export and surveillance., 16th Penn State Symposium in Plant Physiology, Penn State, USA, 18-20 May 2006.
  • Koroleva, O.A.; Pendle, A.F.; Lewandowska, D.; Kim, S.; Brown, J.W.S.; Shaw, P.J. (2006) Function of the exon junction complex in the plant nucleolus., RNA Society Meeting, Seattle, USA, 20-25 June 2006.
  • Kim, S.; Lewandowska, D.; Pendle, A.; Koroleva, O.; Shaw, P.J.; Brown, J.W.S. (2006) Novel functions for the nucleolus from proteomic and RNomic analysis of Arabidopsis nucleoli., RNA Society Meeting. Seattle, USA, 20-25 June 2006.
  • Kim, S.; Ryabov, E.V.; MacFarlane, S.A.; Kalinina, N.O.; Rakitina, D.V.; Gillespie, T.; Brown, J.W.S.; Taliansky, M.E. (2006) Involvement of the nulceolus in Umbravirus long-distance movement., Plasmodesmata 2006, Pitlochry, 30 July - 3 August 2006.
  • Kim, S.; Ryabov, E.V.; Brown, J.W.S.; Taliansky, M.E. (2004) Involvement of the nucleolus in plant virus systemic infection., Post-transcriptional Regulation of Plant Gene Expression, Norwich, 15-17 April 2004.
  • Taliansky, M.E.; Kim, S.; Ryabov, E.V.; Robinson, D.J.; Brown, J.W.S. (2003) Involvement of the Nucleolus in Umbravirus Systemic Infection., XI Congress of International Society for Molecular Plant-Microbe Interactions, St Petersburg, Russia, 18-27 July 2003, pp73-76.
  • Kim, S.; Ryabov, E.; Brown, J.W.S.; Taliansky, M.E. (2003) The intracellular trafficking of the ORF3 protein of Groundnut rosette umbravirus (GRV)., Advances in Plant Virology, AAB Conference, Montpellier, France, September 2003.
  • Stamati, K.; Blackie, S.; Russell, J.R.; Brown, J.W.S. (2002) Small nucleolar RNA (snoRNA) genes as molecular markers for polyploidy and hybridisation., Plant Conservation in Scotland, 2002.
  • Stamati, K.; Blackie, S.; Brown, J.W.S.; Russell, J.R. (2002) Population genetics of sub-Arctic willow (S. lanata, S. lapponum and S. herbacea)., Plant Conservation in Scotland, 2002.
  • 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.

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.