Assistant Professor;
Ph.D., Pennsylvania State University, 2003

POSITIONS AVAILABLE for graduate and undergraduate students (starting in spring of 2010).

Research and Professional Interests:

• Research interests
  Cell fate specification and reprogramming in plants; evolutionary and developmental biology; plant-environment interaction
• Approaches
  Genomics; epigenomics; proteomics; fluorescence-assisted cell sorting (FACS); molecular genetics
• Model systems
  Arabidopsis thaliana; Physcomitrella patens

1. Cell fate specification and reprogramming

A major goal of my research is to elucidate the molecular basis of cell fate specification and reprogramming in plants. To this end, I will determine the global landscape of histone marks in individual cell types in the Arabidopsis root, using the ChIP/chip or ChIP-seq method. The root of Arabidopsis thaliana is best suited to these studies, as it permits isolation of individual cell types by fluorescence-assisted cell sorting (FACS) coupled with cell-type–specific GFP marker lines (1) (Fig. 1). Genes that are marked differently in different cell types will be identified, and their role in cell-fate specification will then be characterized by standard molecular-genetics methods.

Regenerative ability is an ancient trait, but somehow it has been lost in the majority of higher organisms, including humans. Higher plants are an exception, however: a whole plant can be regenerated from differentiated cells. Plant cells are thus believed to be totipotent. What makes plants so special, then? An important clue to this enigma came from a recent study, which showed that in animal stem cells the promoters of cell-fate-determination genes carry both active and repressive histone marks (termed “bivalent marks”), but in differentiated cell types only one of the marks is retained (2). This finding provides a plausible explanation why stem cells are developmentally plastic. It also suggests that totipotency genes in plants may have bivalent marks not only in stem cells but also in differentiated cells. With the cellular-epigenomics approach, we are now in an excellent position to address this important question.

2. Evolutionary and developmental biology

Mosses are among the most primitive land plants; they lack some of the critical features of other land plants such as roots and vascular tissues. Intriguingly, recent sequencing of the Physcomitrella patens genome revealed that this moss has clear homologs to the majority of Arabidopsis genes, including those involved in root development (3). The question is, what is the function of the root-development-related genes in the moss? I will address this question using P. patens as a model system, not only because its genome sequence is now available but also because it is amenable to genetic manipulation. As a matter of fact, P. patens is so far the only plant species with which the homology-based gene-targeting method can be efficiently performed, so it is a very powerful system for molecular evolutionary studies. By determining the function of the moss homologs of root development genes, we would gain significant insight into the origin of root. Physcomitrella will also be used as a model system for characterizing the genes that control totipotency, as generating transgenic plants from a single somatic cell is already routine.

3. Plant-environment interaction

Plants are sessile, and thus, to survive a changing environment, they must be able to adjust their developmental plan accordingly, in addition to mounting a whole array of stress responses. After a short exposure to a mild stress, such as cold, plants also acquire the ability to withstand a higher intensity of the same stress, a phenomenon called acclimation. Evidence indicates that plant hormones play an important role in this process, and one critical component of the regulatory mechanism is epigenetic regulation. Another goal of my research is therefore to reveal how plants integrate various environmental cues into their development program and the molecular basis of adaptation, with a focus on phytohormone signaling and epigenetic regulation.

1. K. Birnbaum et al., Nature Methods 2, 615. 2005.
2. B. E. Bernstein et al., Cell 125, 315. 2006.
3. S. A. Rensing et al., Science 319, 64. 2008.

Cui, H., and P. N. Benfey, 2009. Cortex proliferation: simple phenotype, complex regulatory mechanisms. Plant Signaling and Behavior, 4:551-553.

Cui, H., and P. N. Benfey. 2009. Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root. Plant Journal 58:1016-1027.

Cui, H., M. P. Levesque, T. Vernoux, J. Y. Wang, I. Blilou, B. Scheres, and P. N. Benfey. 2007. An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 316:421-425 (article highlighted in Cell, Nature, Science, STKE, JCB, and C&E News).

Levesque, M. P., T. Vernoux, W. Busch, H. Cui, J. Y. Wang, I. Blilou, H. Hassan, K. Nakajima, N. Matsumoto, J. U. Lohmann, B. Scheres, and P. N. Benfey. 2006. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biology 4:e143.

Cui, H., and N. V. Fedoroff. 2002. Inducible DNA demethylation mediated by the maize Spm transposon-encoded TnpA protein. Plant Cell 14:2883-2899.

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