John W. S. Brown

Research Focus

We are studying alternative splicing and splice site selection in plant intron splicing, and the connection with nonsense-mediated decay. Currently around 25% of Arabidopsis/rice genes are predicted to undergo alternative splicing (that is, 6-8000 genes).

In plants, the functions of alternative proteins from the different transcripts is known for only a handful of genes and virtually nothing is known about the mechanisms by which alternative splice site selection occurs in plants. We are using our expertise in splicing analysis systems and splicing factors/RNA-binding proteins to examine alternative splicing control of individual genes and more global alteration of splicing patterns of alternatively spliced genes.

We have developed a pilot RT-PCR panel containing around 100 alternative splicing events from Arabidopsis to detect changes in splicing pattern in plants grown under different conditions or over-expressing specific proteins. Along with the other plant groups in the NoE (Barta; Jarmolowski) we will extend the RT-PCR panel to include 3-400 alternative splicing events. Ultimately, we aim to establish an alternative splicing microarray for Arabidopsis transcripts but will also examine the utility of tiling arrays.


  1. 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 precursor messenger RNA splicing in multiple gene transcripts. The Plant Journal 53, 1035–1048.
  2. Simpson, C.G., Lewandowska, D., Fuller, J., Maronova, M., Kalyna, M., Davidson, D.,McNicol, J.,, Raczynska, D., Jarmolowski, A., Barta, A., and Brown, J.W.S. (2008). Alternative Splicing in Plants. Biochemical Society Transactions 36(Pt 3), 508-10.
  3. 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)
  4. 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)
  5. 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.
  6. 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.
  7. 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.
  8. Simpson, C. G., Thow, G., Clark, G. P., Jennings, S. N., Watters, J. A. and Brown, J. W. S. (2002). Mutational analysis of a plant branchpoint and polypyrimidine tract required for constitutive splicing of a mini-exon. RNA 8, 47-56.
  9. Simpson, C. G., Hedley, P. E., Watters, J. A., Clark, G. P., McQuade, C. M., Machray, G. C. and Brown, J. W. S. (2000). Requirements for mini-exon inclusion in potato invertase mRNAs provides evidence for exon-scanning interactions in plants. RNA 6, 422-423.

Key lab techniques: in vivo systems for splicing analysis; medium through-put RT-PCR.

Key lab reagents: splicing reporter constructs, gateway clones, expression cDNAs.

Lab contact: Craig Simpson:

Lab website: