Research Spotlight

Dr. Doris Wagner

Department of Biology
University of Pennsylvania

Philadelphia, PA 19104

Research interests: My lab is interested in understanding the regulation of developmental transitions which often necessitate large scale transcriptional reprogramming. Much has been learned about the importance of transcription in development, differentiation and growth. The template for transcription in all eukaryotes is DNA tightly compacted into chromatin. This not only limits accessibility of the DNA for many transcription factors but also adds another layer of regulatory potential: chromatin remodeling and modifying enzymes can differentially alter accessibility of chromosomal DNA in response to endogenous and environmental stimuli. However, the role of chromatin alterations in transcriptional reprogramming is poorly understood. By using genetic enhancer screen of a weak allele of the plant specific transcription factor and master developmental regulator LEAFY, I identified two alleles of an Arabidopsis Snf2-type chromatin remodeling ATPase (Wagner and Meyerowitz, 2002).  The mutant was named splayed (syd) for its conspicuous splayed open flower buds. Subsequent investigation of the in vivo role of SYD and related chromatin remodeling ATPases have begun to shed light on the contribution of these regulators to proper development and growth.

We are interested in understanding the role of chromatin remodeling ATPases in the organism. Snf2 ATPases are part of large protein complexes, which use the energy derived from ATP hydrolysis to disrupt interactions between the DNA and histones thus allowing transcription factors to bind to previously inaccessible motifs in the genomic DNA. The critical importance of chromatin remodeling in normal development is underscored by the identification of Snf2 ATPases and complex components as tumor suppressors for lung, breast and prostate cancers. To gain insight into the role of chromatin remodeling genes, Arabidopsis has a significant advantage. Whereas mutants in these important genes are lethal in most eukaryotes, our studies have shown that two different chromatin remodeling ATPase null mutants (in SYD and in the closest homolog BRAHMA (BRM)) are viable in Arabidopsis (Wagner and Meyerowitz, 2002; Kwon et al., 2006).  This property allows us to study the role of chromatin remodeling throughout development, dramatically extending mechanistic insight into this fundamental process (Wagner, 2003).

Although chromatin remodeling ATPases were considered general transcriptional regulators, we hypothesized that these ATPases may also function as specific regulators that control expression of select sets of genes in distinct pathways. Indeed, we demonstrated that the failure to maintain the stem cell population in the shoot apical meristem of syd null mutants is explained by the direct transcriptional regulation of expression of a single master regulator, the homeodomain transcription factor WUSCHEL (Kwon et al. 2005). This suggests that chromatin remodeling ATPases may regulate a small set of select target genes in a given developmental pathway. We extended this finding using transcription profiling of the chromatin remodeler null mutants (syd and brm) compared to the wild-type. In each mutant only a small number of genes (1-3%) is misregulated compared to wild-type (Bezhani et al., 2007). This number includes both direct targets and indirect downstream effects, suggesting that expression of very few genes is directly controlled by the two chromatin remodelers.

Arabidopsis has multiple SWI/SNF chromatin remodeling ATPases, a feature shared with most multicellular metazoans. The protein most closely related to SYD is BRM (Su et al., 2006). We examined whether SYD and BRM have unique, shared, or redundant roles in a single developmental pathway, cotyledon separation. This process is controlled by the three redundantly acting CUP SHAPED COTYLEDON (CUC) transcription factors. We found that BRM act upstream of all three genes, while SYD acts upstream only of CUC2 (Kwon et al., 2005, Kwon et al., 2006). Thus, SYD and BRM have shared, as well as unique roles in cotyledon separation. This conclusion is further supported by comparative transcript profiling of syd and brm compared to the wild-type (Bezhani et al., 2007), in which we identified groups of genes dependent on either SYD or BRM as well as a significant number of genes dependent on both SWI/SNF ATPases. While our studies have focused on the role and function of Snf2 ATPases in Arabidopsis, enabled by the experimental advantages of this system, our findings are important for deciphering the role of Snf2 ATPases in other multicellular eukaryotes (Kwon and Wagner, 2007).

This framework for the activity of the SYD and BRM SWI/SNF ATPases in Arabidopsis development—which indicates a potential for regulatory events of great specificity, achieved by individual proteins with overlapping activities—provides the foundation for our future investigations in which we focus on three central questions.

Selected Publications:
Bezhani, S., Winter, C., Hershman, S., Wagner, J.D., Kennedy, J.F., Kwon, C.S., Pfluger, J., Su, Y., and Wagner, D. (2007). Unique, Shared, and Redundant Roles for the Arabidopsis SWI/SNF Chromatin Remodeling ATPases BRAHMA and SPLAYED. Plant Cell 19, 403-416.

Kwon, C.S., and Wagner, D. (2007). Unwinding chromatin for development and growth: a few genes at a time. Trends Genet 23, 403-412.

Kwon, C.S., Hibara, K.I., Pfluger, J., Bezhani, S., Metha, H., Aida, M., Tasaka, M., and Wagner, D. (2006). A role for chromatin remodeling in regulation of CUC gene expression in the Arabidopsis cotyledon boundary. Development 133, 3223-3230.

Su, Y., Kwon, C.S., Bezhani, S., Huvermann, B., Chen, C., Peragine, A., Kennedy, J.F., and Wagner, D. (2006). The N-terminal ATPase AT-hook-containing region of the Arabidopsis chromatin-remodeling protein SPLAYED is sufficient for biological activity. Plant J 46, 685-699.

Wagner, D. (2003). Chromatin regulation of plant development. Curr Opin Plant Biol 6, 20-28.

Wagner, D., and Meyerowitz, E.M. (2002). SPLAYED, a Novel SWI/SNF ATPase Homolog Controls Reproductive Development in Arabidopsis thaliana. Current Biology 12, 1-20.