Research
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)
Publications
Journals
- Zhang, R.; Kuo, R.; Coulter, M.; Calixto, C.P.G.; Entizne, J.C.; Guo, W.; Marquez, Y.; Milne, L.; Riegler, S.; Matsui, A.; Tanaka, M.; Harvey, S.; Gao, Y.; Wießner-Kroh, T.; Paniagua, A.; Crespi, M.; Denby, K.; ben Hur, A.; Huq, E.; Jantsch, M.; Jarmolowski, A.; Koester, T.; Laubinger, S.; Li, Q.Q.; Gu, L.; Seki, M.; Staiger, D.; Sunkar, R.; Szweykowska-Kulinska, Z.; Tu, S.; Wachter, A.; Waugh, R.; Xiong, L.; Zhang, X.N.; Conesa, A.; Reddy, A.S.N.; Barta, A.; Kalyna, M.; Brown, J.W.S. (2022) A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis, Genome Biology 23, Art. 149
- Guo, W.; Tzioutziou, N.A.; Stephen, G.; Milne, I.; Calixto, C.P.G.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2021) 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists., RNA Biology, 18, 1574-1587
- Kuo, R.I.; Cheng, Y.; Zhang, R.; Brown, J.W.S.; Smith, J.; Archibald, A.L.; Burt, D.W. (2020) Illuminating the dark side of the human transcriptome with long read transcript sequencing., BMC Genomics, 21, Article No. 751.
- Raxwal, V.K.; Simpson, C.G.; Gloggnitzer, J.; Entinze, J.C.; Guo, W.; Zhang, R.; Brown, J.W.S.; Riha, K. (2020) Nonsense-mediated RNA decay factor UPF1 is critical for posttranscriptional and translational gene regulation in arabidopsis., The Plant Cell, 32, 2725-2741.
- Raczynska, K.D.; Stepien, A.; Kierzkowski, D.; Kalak, M.; Bajczyk, M.; McNicol, J.; Simpson, C.G.; Szweykowska-Kulinska, Z.; Brown, J.W.S.; Jarmolowski, A. (2020) The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana (vol 42, 1224, 2014). Correction., Nucleic Acids Research, 48, 1604-1605.
- Dantas, L.B.; Calixto, C.P.G.; Dourado, M.M.; Carneiro, M.S.; Brown, J.W.S.; Hotta, C.T. (2019) Alternative splicing of circadian clock genes correlates with temperature in field-grown sugarcane., Frontiers in Plant Science, 10, Article No. 1614.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Godoy Herz, M.A.; Kubaczka, M.G.; Brzyzek, G.; Servi, L.; Krzyszton, M.; Simpson, C.; Brown, J.; Swiezewski, S.; Petrillo, E.; Kornblihtt A.R. (2019) Light regulates plant alternative splicing through the control of transcriptional elongation., Molecular Cell, 73, 1066-1074.e3.
- Calixto, C.P.G.; Tzioutziou, N.A.; James, A.B.; Hornyik, C.; Guo, W.B.; Zhang, R.X.; Nimmo, H.G.; Brown, J.W.S. (2019) Cold-dependent expression and alternative splicing of arabidopsis long non-coding RNAs., Frontiers in Plant Science, 10, Article No. 235.
- James, A.B.; Calixto, C.P.G.; Tzioutziou, N.A.; Guo, W.; Zhang, R.X.; Simpson C.G.; Jiang. W.Y.; Nimmo, G.A.; Brown, J.W.S.; Nimmo, H.G. (2018) How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)., Plant Cell and Environment, 41, 1539-1550.
- Calixto, C.P.G.; Guo, W.; James, A.B.; Tzioutziou, N.A.; Entizne, J.C.; Panter, P.E.; Knight, H.; Nimmo, H.G.; Zhang, R.X.; Brown, J.W.S. (2018) Rapid and dynamic alternative splicing impacts the arabidopsis cold response transcriptome., Plant Cell, 30, 1424-1444.
- Guo, W.B.; Calixto, C.P.G.; Brown, J.W.S.; Zhang, R.X. (2017) TSIS: an R package to infer alternative splicing isoform switches for time-series data., Bioinformatics, 33, 3308-3310.
- Gou, W.; Calixtio, C.P.G.; Tzioutziou, N.; Ping, L.; Waugh, R.; Brown, J.W.S.; Zhang, R. (2017) Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size., BMC Systems Biology, 11, Article No. 62.
- Brown, J.W.S.; Calixto, C.P.G.; Zhang, R.X. (2017) High quality reference transcript datasets hold the key to transcript-specific RNA-seq analysis in plants., New Phytologist, 213, 525-530.
- Calixto, C.P.G.; Simpson, C.G.; Waugh, R.; Brown, J.W.S. (2016) Alternative splicing of barley clock genes in response to low temperature., PLoS ONE, 11, Article No. e0168028.
- Russell, J.; Mascher, M.; Dawson, I.K.; Kyriakidis, S.; Calixto, C.; Freund, F.; Bayer, M.; Milne, I.; Marshall-Griffiths, T.; Heinen, S.; Hofstad, A.; Sharma, R.; Himmelbach, A.; Knauft, M.; van Zonneveld, M.; Brown, J.W.S.; Schmid, K.; Kilian, B.; Muehlbauer, G.J.; Stein, N.; Waugh R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation., Nature Genetics, 48, 1024-1030.
- Carvalho, R.F.; Szakonyi, D.; Simpson, C.G.; Barbosa, I.C.R.; Brown, J.W.S.; Baena-Gonzalez, E.; Duque, P. (2016) The arabidopsis SR45 splicing factor, a negative regulator of sugar signaling, modulates SNF1-related protein kinase 1 stability., Plant Cell, 28, 1910-1925.
- Brown, J.W.S.; Simpson, C.; Marquez, Y.; Gadd, G.M.; Barta, A.; Kalyna, M. (2015) Lost in translation: pitfalls in deciphering plant alternative splicing transcripts., The Plant Cell, 27, 2083-2087.
- Zhang, R.X.; Calixto, C.P.G.; Tzioutziou, N.A.; James, A.B.; Simpson, C.G.; Guo, W.B.; Marquez, Y.; Kalyna, M.; Patro, R.; Eyras, E.; Barta, A.; Nimmo, H.G.; Brown, J.W.S. (2015) AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana., New Phytologist, 208, 96-101.
- Gustavo Schlaen, R.; Mancini, E.; Sanchez, S.E.; Perez-Santangelo, S.; Rugnone, M.L.; Simpson, C.G.; Brown, J.W.S.; Zhang, X.; Chernomoretz, A.; Yanovsky, M.J. (2015) The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms., Proceedings of the National Academy of Sciences of the United States of America (PNAS), 112, 9382-9387.
- Shin, K.H.; Yang, S.H.; Lee, J.Y.; Lim, C.W.; Lee, S.C.; Brown, J.W.S.; Kim, S.H. (2015) Alternative splicing of mini-exons in the Arabidopsis leaf rust receptor-like kinase LRK10 genes affects subcellular localisation., Plant Cell Reports, 34, 495-505.
- Igartua, E.; Mansour, E.; Cantalapiedra, C.P.; Contreras-Moreira, B.; Gracia, M.P.; Fuster, P.; Escribano, J.; Molina-Cano, J.L.; Moralejo, M.; Ciudad, F.J.; Thomas, W.T.B.; Karsai, I.; Casas, A.M. (2015) Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information., Molecular Breeding, 35, Article No. 11.
- Calixto, C.P.G.; Waugh, R.; Brown, J.W.S. (2015) Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes., Journal of Molecular Evolution, 80, 108-119.
- Simpson, C.G.; Lewandowska, D.; Liney, M.; Davidson, D.; Chapman, S.; Fuller, J.; McNicol, J.; Shaw, P.; Brown, J.W.S. (2014) Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially., New Phytologist, 203, 424-436.
- Bardou, F.; Ariel, F.; Simpson, C.G.; Romero-Barrios, N.; Laporte, P.; Balzergue, S.; Brown, J.W.S.; Crespi, M. (2014) Long noncoding RNA modulates alternative splicing regulators in Arabidopsis., Developmental Cell, 30, 166-176.
- Petrillo, E.; Herz, M.A.G.; Fuchs, A.; Reifer, D.; Fuller, J.; Yanovsky, M.J.; Simpson, C.; Brown, J.W.S.; Barta, A.; Kalyna, M.; Kornblihtt, A.R. (2014) A chloroplast retrograde signal regulates nuclear alternative splicing., Science, 344, 427-430.
- Haling, R.E.; Brown, L.K.; Bengough, A.G.; Valentine, T.A.; White, P.J.; Young, I.M.; George, T.S. (2014) Root hair length and rhizosheath mass depend on soil porosity, strength and water content in barley genotypes., Planta, 239, 643-651.
- Staiger, D.; Brown, J.W.S. (2013) Alternative splicing at the intersection of biological timing, development, and stress responses., The Plant Cell, 25, 3640-3656.
- Lewandowska, D.; ten Have, S.; Hodge, K.; Tillemans, V.; Lamond, A.I.; Brown, J.W.S. (2013) Plant SILAC: Stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics., PLoS ONE, 8, Article No. e72207.
- Streitner, C.; Simpson, C.G.; Shaw, P.; Danisman, S.; Brown, J.W.S.; Staiger, D. (2013) Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana., Plant Signalling and Behaviour, 8, Article No. e24638.
Books / chapters
- 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
- 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.
Technical / contract reports
- 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.
Conference papers
- 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.; 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.
Conference posters / abstracts
- Rapazote-Flores, P.; Mayer, C-D.; Hedley, P.E.; Morris, J.; Fuller, J.; Milne, L.; Stephen, G.; Raeside, A.; Bayer, M.; Brown, J.W.S.; Calixto, C.P.G.; de la Vega, J.; Ayling, S.; Sampath, D.; Caccamo, M.; Waugh, R. (2016) Organ specific expression and alternative splicing in Barley (Hordeum vulgare)., Poster, September 2016.
- Runxuan, Z.; Calixto Cristiane, P.G.; Tzioutziou, N.A.; James, A.B.; Simpson, C.G.; Guo, W.; Marquez, Y.; Kalyna, M.; Patro, R.; Eyras, E.; Barta, A.; Nimmo. H.G.; Brown, J.W.S. (2015) A comprehensive and non-redundant transcript reference enables accurate quantification of transcript-specific expression in Arabidopsis thaliana., Plant Genomes and Biotechnology: from Genes to Networks, Cold Spring Harbor lab., Long Island, USA, 2-5 December 2015.
- 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).
- Lewandowska, D.; Ten Have, S.; Hodge, K.; Tillemans, V.; Lamond, A.I.; Brown, J.W.S. (2013) Plant SILAC: stable-isotope labelling with amino acids of Arabidopsis seedlings for quantitative proteomics., Computational Mass Spectrometry-Based Proteomics – 5th MaxQuant Summer School 2013, Martinsried, Munich, Germany, 23-28 June 2013 (Poster).
- 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).
- Lewandowska, D.; Ten Have, S.; Hodge, K.; Brown, J.W.S. (2012) Efficient labelling of Arabidopsis seedlings by SILAC., Proteomics Bioinformatics Advance Course 2012, Cambridge, 5-9 November 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).
- 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).
- Taliansky, M.; Shaw, J.; Kim, S.H.; Ryabov, E.; Kalinina, N.; MacFarlane, S.; Brown, J.W.S. (2011) The nucleolus and plant virus infections., The XV International Congress of Virology, Sapporo, Japan, 6-16 September 2011.
- Taliansky, M.; Shaw, J.; Kim, S.H.; Ryabov, E.; Kalinina, N.; MacFarlane, S.; Brown, J.W.S. (2011) Role of Cajal bodies in plant virus infections., First International SFB 796 Symposium, Mechanisms of Viral Host Cell Manipulation – From Plants to Humans, Bamberg, Germany 2-4 October 2011.
- 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.; 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).
- 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).