Professor of Biology and Graduate Chair in Biology

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Contact Information

University of Pennsylvania School of Arts and Sciences
Department of Biology
103G Carolyn Lynch Laboratory
Philadelphia, PA 19104
Office: 215-898-0483

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Research Interest

Our research focuses on the reprogramming of cell identity and function during developmental transitions and in response to the environment in plants. These sessile organisms are an excellent experimental system to address this question as they need to tailor their final form and cell function to a changing environment for optimal growth and survival. We found that key transcriptional factors, altered hormone environments and changes in the chromatin state together orchestrate this cell reprogramming.

Contributions to Science

The role and Regulation of SWI/SNF chromatin remodeling complexes in plants.

ATP-dependent chromatin remodeling can change the chromatin state by using the energy derived from ATP hydrolysis to altering histone/DNA interactions. We uncovered key roles for plant SWI/SNF subfamily remodelers in stem cell maintenance and in overcoming Polycomb repression for induction of the floral homeotic genes during flower pattering. We have established, genome-wide, the gene expression programs that depend on the SWI/SNF chromatin remodelers. Finally one for the SWI/SNF remodelers, BRM, is critical for water stress response and drought tolerance.

  1. Kwon, C.S., Chen, C., and Wagner, D. (2005). WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis. Genes Development 19, 992-1003.
  2. 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.
  3. Han, S.K., Sang, Y., Rodrigues, A., BIOL425F2010, B., Rodriquez, P.L. and Wagner, D. (2012) The SWI2/SNF2 chromatin remodeling ATPase BRAHMA represses Abscisic Acid Responses in the Absence of the Stress Stimulus in Arabidopsis, Plant Cell 24 4892-4906.
  4. Wu, M.F., Sang, Y., Bezhani, S., Yamaguchi, N., Han, S.K., Li, Z., Su, Y., Slewinski, T.L., and Wagner, D. (2012). SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proceedings of the National Academy of Sciences of the United States of America 109, 3576-3581. (faculty 1000 recommended)


The switch to flower formation, a major developmental switch critical for reproductive success.

Plants generate different types of lateral organs (leaves, then branches and finally flowers) post-embryonically from stem cell descendants at the shoot apex. When flowers form is critical for plant reproductive success. If flowers form too soon, not enough resources may have accumulated to support seed formation; if they form too late, plants may not be able to complete their lifecycle before the winter. Our research has established that the plant specific helix-turn-helix transcription factor LEAFY is a key regulator of the timing of flower formation. We identified the regulatory network downstream of LFY using genetic and genomic approaches. These studies have identified a set of interlocking feed-forward loops that together control the timing of the upregulation of the expression of the direct LFY target APETALA1, a commitment factor of floral fate. More recently, we showed that LFY plays an active role changing the hormone environment in newly formed primordia to promote floral fate.

  1. William, D.A., Su, Y., Smith, M.R., Lu, M., Baldwin, D.A., and Wagner, D. (2004). Genomic identification of direct target genes of LEAFY. Proceedings of the National Academy of Sciences of the United States of America 101, 1775-1780.
  2. Yamaguchi, A., Wu, M.F., Yang, L., Wu, G., Poethig, R.S., and Wagner, D. (2009). The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Developmental Cell 17, 268-278. (faculty 1000 recommended)
  3. Winter, C.M., Austin, R.S., Blanvillain-Baufume, S., Reback, M.A., Monniaux, M., Wu, M.F., Sang, Y., Yamaguchi, A., Yamaguchi, N., Parker, J.E., J.E., Parcy, F., Jensen, S.T., Li, H., Wagner, D. (2011). LEAFY Target Genes Reveal Floral Regulatory Logic, cis Motifs, and a Link to Biotic Stimulus Response. Developmental Cell 20, 430-443.
  4. Yamaguchi, N., Winter, C., Wu, M-F., Kanno, Y., Yamaguchi, A., Seo, M., and Wagner, D. (2014) Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science 344, 638-41. (faculty 1000 recommended) (Science editor’s choice).

Organogenesis and differentiation in response to hormonal cues

We have recently become interested in the question how hormone responses control organogenesis and differentiation. We have identified the gene regulatory network activated by the plant hormone auxin during organogenesis (flower primordium initiation) and uncovered the mechanism required for auxin-directed gene activation in the context of chromatin. In addition, we have elucidated the transcriptional and hormonal changes that underlie maturation of plant organs.

  1. Yamaguchi, N., Wu, M.-F., Winter, C., Berns, M., Nole-Wilson, S., Yamaguchi, A., Coupland, G., Krizek, B., and Wagner, D. (2013) Auxin-mediated Initiation of the Flower Primordium. Developmental Cell 24, 1–12. (faculty 1000 recommended)
  2. Efroni, I., Han, S.K., Kim, H.Y., Wu, M.F., Sang, Y., Hong, J.C., Eshed, Y*., and Wagner, D*. (2013). Regulation of leaf maturation by chromatin-mediated modulation of hormonal responses. Developmental Cell. 24, 438-445. *corresponding authors
  3. Wu, M-F, Yamaguchi, N., Xiao J., Bargmann, B. Estelle, M., Sang, Y. and Wagner, D. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate eLife 2015;4:e09269 (faculty 1000 recommended)