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John Brown

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Staff picture: John Brown
Head of University of Dundee Division of Plant Sciences
John.Brown@hutton.ac.uk
+44 (0)844 928 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 

  • Canetta, E., Kim, S.H., Kalinina, N.O., Shaw, J., Adya, A.K., Gillespie, T. Brown, J.W.S. and Taliansky, M. 2008. A plant virus movement protein forms ring-like complexes with the major nucleolar protein, fibrillarin, in vitro. Journal of Molecular Biology 376(4), 932-7.
  • Simpson, C.G. and Brown, J.W.S. 2008. Plant U12-dependent (AT-AC) introns. In: 'Nuclear pre-mRNA processing in plants'. Ed. Reddy, A.S N. (in press).
  • Brown, J.W.S. and Shaw, P.J. 2008. The plant nucleolus and mRNA biogenesis. In: 'Nuclear pre-mRNA processing in plants'. Ed. Reddy, A.S.N. (in press).
  • Simpson, C.G., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Barta, A. and Brown, J.W.S. 2008. Monitoring changes in alternative pre-mRNA splicing in multiple gene transcripts. Plant Journal (Accepted article online: 15 December 2007).
  • Kim, S.H., MacFarlane, S., Kalinina, N.O., Rakitina, D.V., Ryabov, E.V., Gillespie, T., Haupt, S., Brown, J.W.S. and Taliansky M. 2007. Interaction between a plant virus-encoded protein and the major nucleolar protein, fibrillarin, is required for virus systemic infection. Proceedings of the National Academy of Sciences USA 104, 11115-11120.
  • Kim, S.H., Ryabov, E.V., Kalinina, N.O., Rakitina, D.V., MacFarlane, S., Gillespie, T., Haupt, S., Brown, J.W.S. and Taliansky M. 2007. Cajal bodies and the nucleolus are required for systemic infection of a plant virus. The EMBO Journal 26, 2169-2179.
  • Brown, J.W.S., Shaw, P.J., Shaw, P. and Marshall, D.F. 2005. The Arabidopsis nucleolar protein database. Nucleic Acids Research 33, D633-D636.
  • Pendle, A.F., Clark, G.P., Boon, R., Lewandowska, D., Lam, Y.W., Andersen, J., Mann, M., Lamond, A.I., Brown, J.W.S. and Shaw, P.J. 2005. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Molecular Biology Cell 16, 260-269.
  • Shaw, P.J. and Brown, J.W.S. 2004. Plant nuclear bodies. Current Opinion in Plant Biology 7, 614-620.
  • Kim, S.H., Ryabov, E.V., Brown, J.W.S. and Taliansky, M. 2004. Involvement of the nucleolus in plant virus systemic infection. Biochemical Society Transactions 32, 557-560.
  • Lewandowska, D., Simpson, C.G., Clark, G.P., Jennings, S.N., Barciszewska-Pacak, M., Lin, C.-F., Makalowski, W., Brown, J.W.S. and Jarmolowski, A. 2004. Determinants of plant U12-dependent intron splicing efficiency. Plant Cell 16, 1340-1352.  
  • Simpson, C.G., Jennings, S.N., Clark, G.P., Thow, G. and Brown, J.W.S. 2004. Dual functionality of a plant U-rich intronic sequence element. Plant Journal 37, 82-91.
  • Brown, J.W.S. 2003. Echeverria, M., Qu, L.-H., Lowe, T. M., Bachellerie, J.-P., Huettenhofer, A., Kastenmayer, J.P., Green, P.J., Shaw, P. and Marshall, D.F., Plant snoRNA databaseNucleic Acids Research 31, 432-435.
  • Brown, J.W.S., Echeverria, M. and Qu, L.-H. 2003. Plant snoRNA genes: functional evolution and new modes of gene expression. Trends in Plant Science 8, 42-49.
  • Brown, J.W.S., Simpson, C.G., Thow, G., Clark, G.P., Jennings, S.N., Medina-Escobar, M., Haupt, S., Chapman, S.C. and Oparka, K.J. 2002. Splicing signals and factors in plant intron removal. Biochemical Society Transactions 30, 146-149.
  • Kmieciak, M., Simpson, C.G., Lewandowska, D., Brown, J.W.S. and Jarmolowski, A. 2002. Cloning and characterisation of two subunits of Arabidopsis thaliana nuclear cap-binding complex. Gene 283, 171-183.

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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  • Phone: +44 (0)844 928 5428
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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.