• Plant responses to biotic and abiotic stress
• Gene network inference
• MicroRNA regulation in gene expression

Plant stress response

A major project in the laboratory is investigating the responses of plants to biotic (pathogens) and abiotic (ozone, temperature, chemicals) stresses using DNA microarray gene expression profiling and reverse genetics.

We have identified more than 1200 stress-modulated Arabidopsis genes and studying their expression under various conditions.

The illustration at left shows the change in gene expression of 366 genes that are induced (red) or repressed (green) by ozone.

Among the genes induced by various stresses are signaling genes, transcription factors, and effector genes that include enzymes that alter the cells structure and properties in response to stress.

The signaling molecules include MAP kinases and receptor-like kinases.

We are suppressing and overexpressing potential regulatory genes to identify the genes under their control.

We want to understand the structure of the stress-response gene networks and to explores molecular genetic approaches to modifying the stress response (see Holter et al, 2000, 2001).

Hormone responses

The hyl1 Arabidopsis mutant (below left) has a transposon insertion mutation in a gene that is involved in several hormonal signaling pathways, including those for abscisic acid, auxin and cytokinin.

The mutant is affected in many growth parameters, including graviperception.

It is not as sensitive to exogenous auxins and cytokinins as the wiltype, but it is hypersensitive to abscisic acid.

The HYL1 protein binds to double-stranded RNA and localizes to the nucleus.

The mutant is described in Lu and Fedoroff (2000).

We are investigating how this protein affects hormone signaling.

Transposable elements

Transposable elements or transposons were discovered in corn (maize) plants by the famous geneticist Barbara McClintock through classical genetic analysis of unstable mutations (for a brief history, see http://www.ergito.com or Fedoroff 2001).

Maize transposons were cloned in our laboratory almost 20 years ago and are now widely used for insertional mutagenesis.

We have created a database of several hundred Arabidopsis transposon insertion lines using a transposon tagging system developed in the laboratory (Smith et al., 1996; Raina et al., 2001).

View a map of the insertion sites.

Epigenetic mechanisms

The maize Suppressor-mutator (Spm) transposon is epigenetically inactivated by methylation and encodes a protein, TnpA, which is capable of reversing the inactivation (Schläppi et al., 1994; Fedoroff et al., 1995).

Using an inducible promoter to express TnpA, current experiments seek to understand how it demethylates the Spm promoter.

Some ideas about plant transposon evolution are explored in Fedoroff (2000).

Technical publications

• Racunas, S.A., Shah, N. H., Albert I. and Fedoroff N. V. (2004). HyBrow: A prototype system for computer-aided hypothesis evaluation. Bioinformatics, 20 (Suppl. 1): i257-i264.
• Han, M.H., Goud, S., Song, L., and Fedoroff, N. (2004) The Arabidopsis dsRNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc. Natl. Acad. Sci. USA, 101: 1093-1098.
• Zhang, S. Raina, S., Li, H., Li, J. Ma, H., Huang, H., and N. Fedoroff (2003). Resources for targeted insertional and deletional mutagenesis in Arabidopsis. Plant Mol. Biol. 53: 133-150.
• Shah, N. H., King, D. C., Shah, P. N. and Fedoroff, N. V. (2003) A tool-kit for cDNA microarray and promoter analysis. Bioinformatics, 19: 1848-8.
• Racunas, S.A., N. Shah & N.V. Fedoroff (2003). A contradiction-based framework for testing gene regulation hypotheses. In IEEE Bioinformatics. Stanford University, Palo Alto, California: IEEE Computer Society.
• Mahalingam, R., and Fedoroff, N (2003). Stress response, cell death and signaling: the many faces of ROS. Physiologia Plantarum, 119:56-68.
• Mahalingam, R., Buitrago, A. M., Eckardt, N., Shah, N., Guevara-Garcia, A., Day, P, Raina, R., and Fedoroff, N (2003). Charactarizing the stress/defense transcriptome of Arabidopsis. Genome Biology 4: R20.
• Lu, C., Han, M.H., Guevara-Garcia, A., and Fedoroff, N. Â (2002) Mitogen-activated protein kinase signaling in post-germination arrest of development by abscisic acid. Proc. Natl. Acad. Sci. USA 99:15812-15817.
• Cui, H., and Fedoroff, N. V. (2002) Inducible DNA demethylation mediated by the maize Spm transposon-encoded TnpA protein. Plant Cell 14:1-17.
• Fedoroff, N. V. and W. Fontana (2002) Small numbers of large molecules. Â Science 297:1129-1130.
• Raina, S., Mahalingam, R., Chen, F., and N. Fedoroff (2002). A collection of sequenced and mapped Ds transposon insertion sites in Arabidopsis thaliana. Plant Mol.Biol. 50:93-110.
• Fedoroff, N. V. (2002). RNA-binding proteins in plants: the tip of an iceberg? Curr. Op. Plant Biol., 5:452-459.
• Fedoroff, N. V. (2001) How transposition was discovered. Nature Struct. Biol. 8: 300-301.
• Holter, N. S., Maritan, A., Cieplak, M., Fedoroff, N. V., and J. R. Banavar (2001). Dynamic modeling of gene expression data. Proc. Natl. Acad. Sci. USA, 98: 1693-1698.
• Lu, C. and N. Fedoroff (2000). HYL1, a dsRNA-binding nuclear regulatory protein in plant hormone signaling. Plant Cell 12: 1-15.
• Holter, N. S., Mitra, M., Maritan, A, Cieplak, M., Banavar, J. R. and N. Fedoroff (2000). Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc. Natl. Acad. Sci. USA 97: 8409-8414.
• Fedoroff, N. V. (2000). Transposons and genome evolution in plants. Proc. Natl. Acad. Sci. USA 97: 7002-7007.

Websites and non-technical publications

• Fedoroff, N. V., and N. M. Brown (2004) Mendel in the Kitchen: A Scientist's View of Genetically Modified Foods (NAS Joseph Henry Press: Washington, DC).
• Fedoroff, N. (2003) Prehistoric GM corn. Science 302:1158-59.
• Responses to letters to the editor. Science 303.1765.
• Fedoroff, N. (2001). Biotechnology and agriculture: promise and peril. In: Proceedings of a conference titled: The Role of New Technologies in Poverty Alleviation and Sustainable Development, NAS, in press.
• Fedoroff, N. V. (2001). What is the future of GMOs? In: 2001 AAAS Science and Technology Policy Yearbook. A. H. Teich, S. D. Nelson, C. McEnaney, and S. J. Lita, eds. (AAAS, Washington, D.C.) pp. 165-172.
• Fedoroff, N. V. (2001). The genomicist's tool kit: DNA cloning and sequencing, the polymerase chain reaction, and DNA microarrays. Penn State Science.
• Fedoroff, N. V. (2001). Monsters or miracles? Genetically modified organisms in our food. Penn State Science.
• Fedoroff, N. V. and J. E. Cohen (1999). Plants and population: Is there time? Proc. Natl. Acad. Sci USA 96: 5903-5907.
• Fedoroff, N. (1997). Food for a hungry world: we must find ways to increase agricultural productivity. The Chronicle of Higher Education 43: 84-85.
• Fedoroff, N. (1996). Two women geneticists. American Scholar 65,587-592.
• Fedoroff, N. (1992). Barbara McClintock: the geneticist, the genius, the woman. Cell, 71, 181-182.