Research Interests Systems biology research in Arabidopsis
Our laboratory focuses on the identification and characterization of functional genes influencing plant growth and development. Systems biology approaches as illustrated in Figure 1 have been applied in our laboratory to put these genes and their gene products into the context of Arabidopsis growth and development.
Figure 1: Integration of conventional and high-throughput research for the studies of plant functional genes.
I.The pursuit of hidden components in Arabidopsis light signaling network
Our prime interest is to understand the gene regulation networks underlying the light-regulated morphogenesis processes in plants. The light-mediated morphogenesis processes are the conclusions of gene expression and interactions. We are focusing on multiple layers of expression regulation for light-responsive genes, including transcriptional activation, post-translational modification and protein-protein interactions etc. It is our goal to address the biological functions of these genes/proteins in the Arabidopsis photomorphogenesis processes based on our current and future research.
LZF1 represents one of such genes functioning downstream of HY5 in regulating photomorphogenesis, anthocyanin accumulation and early chloroplast development (Figure 2). We have also identified LWD1 and LWD2 being the newly added components in sensing photoperiod by modulating the Arabidopsis circadian rhythm (Figure 3).
Figure 2: A working model of the role of LZF1 in light signal transduction
Figure 3: Two WD-repeat proteins, LWD1 and LWD2, function in photoperiod sensing.
II.Information-driven research
Our research group also actively applies bioinformatic approach to dissect pre-existing biological questions or to discover novel biological phenomena. The exponential increase of in silico information offers a golden opportunity in expanding the scope of biological research. We have been integrating an experimental loop comprising information gathering, model projection (computing algorithm) and hypothesis testing (wet-bench validation) to address biological questions of our interests. One example of applying this system biology approach in our group was the identification and validation of the cascade production of trans-acting siRNA (tasiRNA) in Arabidopsis (Figure 4).
Figure 4: A model representing a tandem small RNA cascade initiated by the miR173-targeted cleavage.
Liu P.-F., Chang W.-C., Wang Y.-K., Munisamy S.-B., Hsu S.-H., Chang H.-Y., Wu S.-H. and Pan R.-L. (2007) Differential regulation of Ku gene expression in etiolated mung bean hypocotyls by auxins. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1769, 443-454
Chen H.-M., Li Y.-H. and Wu S.-H(2007) Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc. Natl. Acad. Sci. USA 104, 3318-3323
Buchanan-Wollaston V., Page T., Harrison E., Breeze E., Lim P.O., Nam H.G., Lin J.-F., Wu S.-H., Swidzinski J., Ishizaki K., and Leaver C. (2005) Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation induced senescence in Arabidopsis. Plant J. 42, 567-85
Lin J.-F, Wu S.-H (2004) Molecular events in senescing Arabidopsis leaves.
Plant J. 39, 612-628
Lai C.-P, Lee C.-L, Chen P.-H, Wu S.-H, Yang C.-C and Shaw J.-F (2004) Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiol. 134, 1586-1597
Wu S.-H, Ramonell K., Gollub J, Somerville S. C. (2001) Plant gene expression profiling with DNA microarrays. Plant Physiol. Biochem. 39, 917-926.
Wu S.-H and Lagarias J. C. (2000) Defining the Bilin Lyase Domain: Lessons from the Extended Phytochrome Superfamily. Biochemistry 39, 13487-13495.
