Ph.D., University of California, Berkeley, 1995
transcriptional regulation of developmental transitions; role of chromatin remodeling in inducible gene expression
Developmental transition to reproductive development
My lab is interested in understanding at the molecular level the complex changes that occur when an organism switches developmental programs. Specifically, we investigate the transition from vegetative to reproductive development in the plant model system Arabidopsis thaliana. Onset of flower formation triggers a transition from biomass and resource production in the leaves and branches to allocation of these resources to the next generation in the flowers. Timing of this switch and subsequent flower development are therefore not only vital for plant survival, but also critical for human sustenance and biofuel production. Because of its central importance, many external signals (such as temperature and day length) as well as internal cues input into the timing of reproductive development. Upon perception of the required inductive signals cells at the flanks of the stem-cell-pool containing shoot apical meristem give rise to flowers instead of leaves and secondary stems. My lab is interested in identification of the relevant cues and how they are sensed and integrated to result in transcriptional changes that direct altered cell fate and developmental programs. Much of our work has focused on the plant specific helix-turn-helix transcription factor LEAFY (LFY), which plays a critical role in these processes.
Chromatin remodeling and inducible gene expression
The developmental processes we study and other events in the life of a plant that require a switch in survival programs occur in the context of chromatin. Not surprisingly, we have uncovered important roles for proteins that can alter the chromatin state in stimulus-mediated transcriptional reprogramming. One central mechanism for altering the chromatin state is chromatin remodeling, a process that uses the energy derived from ATP hydrolysis to change the interaction between the genomic DNA and the histone octamer in the nucleosome. SWI/SNF ATPases can act in opposition to Polycomb repression, another key mechanism for controlling the activity of genes in euchromatin. My lab is investigating the question how the activity of SWI/SNF chromatin remodelers or Polycomb repressive complexes is regulated to enable them to direct correct cell-type and stimulus-specific chromatin changes.
We use a wide range of approches including genetics, genomics, computational biology, biochemistry and cell biology.
Current and Future Research Projects
1. Cell function reprgramming by abiotic stress
2. Regulation of the switch to flower formation, flower primordium initiation, flower meristem development and flower patterning.
3. Biological roles and regulation of SWI/SNF ATPases.
4. Regulation Polycomb Complex recruitment and activity.
BIOL 101: Introductory Biology
BIOL 483: Epigenetics
Wagner, D. (2017). Key developmental transitions during flower morphogenesis and their regulation. Curr Opin Genet Dev 45, 44-50.
Xiao, J., Jin, R., and Wagner, D. (2017). Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 18, 88.
Xiao, J., Jin, R., Yu, X., Shen, M., Wagner, J.D., Pai, A., Song, C., Zhuang, M., Klasfeld, S., He, C., Santos, A. M., Helliwell, C., Pruneda-Paz, J. L., Kay, S. A., Lin, X., Cui, S., Garcia, M. F., Clarenz, O., Goodrich, J., Zhang, X., Austin, R. S., Bonasio, R., Wagner, D. (2017). Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet. doi:10.1038/ng.3937 https://www.eurekalert.org/pub_releases/2017-08/uop-pbs082117.php
Bossi, F., Fan, J., Xiao, J., Chandra, L., Shen, M., Dorone, Y., Wagner, D., and Rhee, S.Y. (2017). Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. BMC Genomics 18, 480.
Xiao, J., Lee, U.S., and Wagner, D. (2016). Tug of war: adding and removing histone lysine methylation in Arabidopsis. Curr Opin Plant Biol 34, 41-53.
D. Weijers and D. Wagner (2016) Transcriptional responses to the auxin hormone. Annual Reviews of Plant Biology 27(1).
Wagner, D. (2016). Making Flowers at the Right Time. Dev Cell 37, 208-210.
N. J. Provart et al. (2016) 50 years of Arabidopsis research: highlights and future directions. New Phytol. 201 (3):921-44
Peirats-Llobet, M*. , Han, S-K*, Jeong CW, Gonzalez-Guzman, M, Rodriguez, L, Belda-Palazon, B, Wagner, D**and Rodriguez, PL** (2016) A direct link between abscisic acid sensing and the chromatin remodeling ATPase BRAHMA via core ABA signaling pathway components, Molecular Plant 9 (1):136-47. * equal contribution ** corresponding authors
Yamaguchi N, Jeong CW, Nole-Wilson S, Krizek BA, and Wagner D (2016) AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 induce LEAFY expression in response to auxin to promote the onset of flower formation in Arabidopsis. Plant Physiology (1):283-93.
Wu MF*, Yamaguchi N*, Xiao J*, Bargmann B, Estelle M, Sang Y, and Wagner D (2015) Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. eLife 4:e09269. * equal contribution. (faculty 1000 recommended) http://www.eurekalert.org/pub_releases/2015-10/uop-ph101315.php
Xiao, J. and Wagner D. (2015) Polycomb repression in the regulation of growth and development in Arabidopsis. Current Opinion in Plant Biology 23:15-24.
De Rybel, B., Adibi, M., Breda, A.S., Wendrich, J.R., Smit, M.E., Novak, O., Yamaguchi, N., Yoshida, S., Van Isterdael, G., Palovaara, J Nijsse, B., Boekschoten, M. V., Hooiveld, G., Beeckman, T., Wagner, D., Ljung, K., Fleck, C., Weijers, D. (2014). Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis. Science 345,1255215.
Xiao, J., Xu, S., Li, C., Xu, Y., Xing, L., Niu, Y., Huan, Q., Tang, Y., Zhao, C., Wagner, D., Gao, C., Chong, K. (2014). O-GlcNAc-mediated interaction between VER2 and TaGRP2 elicits TaVRN1 mRNA accumulation during vernalization in winter wheat. Nature communications 5, 4572.
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. (Editor's choice http://stke.sciencemag.org/content/7/325/ec127) http://www.eurekalert.org/pub_releases/2014-05/uop-phh050814.php
Efroni, I., Han, S.K., Kim, H.J., Wu, M.F., Sang, Y., Steiner, E., Hong, J.C., Eshed, Y*., and Wagner, D*. (2013). Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Developmental Cell 24, 438-445. * corresponding authors
Yamaguchi, N., Wu, M.-F., Winter, C., Berns, M., Nole-Wilson, S., Yamaguchi, A., Coupland, G., Krizek, B., and Wagner, D. (2013). A Molecular Framework for Auxin-mediated Initiation of Flower Primordia. Developmental Cell 24, 1–12.
Han, S.K., Sang, Y., Rodrigues, A., BIOL425F2010, Wu, M.F., 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 2012;24 4892-4906.
EPIC Planning Committee (2012) (Wagner D. corresponding author). Reading the second Code: Mapping Epigenomes to understand Plant Growth, Development and Adaptation to the Environment. Plant Cell 24 (6) 2257-2261.
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.
Pastore, J.J., Limpuangthip, A., Yamaguchi, N., Wu, M.F., Sang, Y., Han, S.K., Malaspina, L., Chavdaroff, N., Yamaguchi, A., and Wagner, D. (2011). LATE MERISTEM IDENTITY2 acts together with LEAFY to activate APETALA1. Development 138, 3189-3198.
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.
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.