Professor, D.J. Sibley Centennial Professor in Plant Molecular Genetics

Ph.D. Texas A& M University

zjchen@mail.utexas.edu

Office NMS 3.122

(512) 475-9327

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We study genetic and epigenetic mechanisms for gene expression changes in polyploids. Polyploidy, or whole-genome duplication (WGD), is an evolutionary innovation for all eukaryotes including some animals and many plants. The common occurrence of polyploidy suggests an evolutionary advantage of having multiple sets of genetic material for adaptive evolution. However, increased gene and genome dosages in autopolyploids (duplication of a single genome) and allopolyploids (combination of two or more divergent genomes) often cause genomic instabilities, chromosomal imbalances, regulatory incompatibilities, and reproductive failures. Aneuploid and polyploid cells in animals and humans are often associated with carcinogenesis. Therefore, new polyploids must establish a compatible relationship between alien cytoplasm and nuclei and among divergent genomes, leading to rapid changes in genome structure, gene expression, and developmental traits such as fertility, inbreeding, apomixis, flowering time, and hybrid vigor. The underlying mechanisms for these changes are poorly understood. We employ genetic and biochemical approaches in combination with DNA microarrays, deep-sequencing, and bioinformatic tools to investigate how changes in DNA sequences, cis- and trans-acting factors, chromatin modifications, RNA-mediated pathways, and regulatory networks modulate silencing and activation of homoeologous genes, giving rise to phenotypic variation in polyploid plants and agricultural crops, many of which have increased biomass and enhanced traits. Elucidating mechanisms for polyploidy may ultimately reveal new approaches to reactivate or silence endogenous genes and lead the way to improve future applications of biotechnology in agriculture and medicine.

Selected Publications

Tian, L. and Chen, Z. J. (2001). Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci. USA 98:200-205.

Lee, H.-S. and Chen, Z. J. (2001). Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98:6753-6758.

Wang, J., Lee, H.-S., Tian, L., Chen, M., Lee, J. J., Madlung, A., Comai, L., and Chen, Z. J. (2004). Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1861-1973.

Tian, L., Fong, M. P., Wang, J. J., Wei, N. E., Jiang, H., Doerge, R. W., and Z. J. Chen (2005). Reversible histone acetylation and deacetylation mediate dynamic changes in plant gene regulation and development. Genetics 169:337-345.

Yang, S. S., Cheung, F., Lee, J. J., Ha, M., Wei, E. N., Sze, S.-H., Stelly, D. M., Thaxton, P. M., Triplett, B. A., Town, C. D., and Chen, Z. J. (2006). Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant Journal 47:761-775.

Chen, Z. J. (2007). Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Ann Rev. Plant Biol. 58: 377-406.

Ha, M., Li, W.-H., and Z. J. Chen (2007). External factors accelerate expression divergence between duplicate genes. Trends in Genet. 23:162-166.

Lee, J., Woodward, A. W., and Chen, Z. J. (2007) Gene expression changes and early events in cotton fiber development. Annals of Botany 100:1391-1401.

Chen, Z. J., Scheffler, B. E., Dennis, E., Triplett, B. A., Zhang, T., Chen, X., Stelly, D. M., Rabinowicz, P. D., Town, C. D., Arioli, T., Brubaker, C., Cantrell, R. G., Lacape, J. M., Ulloa, M., Chee, P., Gingle, A. R., Haigler, C. H., Percy, R., Saha, S., Wilkins, T., Wright, R. J., Van Deynze, A., Zhu, Y., Yu, S., Guo, W., Abdurakhmonov, I., Katageri, I., Ananda-Kumar, P., Rahman, M., Yusuf Zafar, Y., Yu, J. Z., Kohel, R. J., Wendel, J. F., and Paterson, A. H. (2007) Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145:1303-1310.

Chen, M., Ha, M., Lackey, E., Wang, J., and Chen, Z. J. (2008) RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 178:1845-1858.

Ni, Z., Kim, E., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z. J. (2009) Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids. Nature 457:327-331.

Ha, M., Lu, J., Tian, L., Ramachandran, V., Kasschau, K. D., Chapman, E. J., Carrington, J. C., Chen, X., Li, W.-H., Wang, X., and Chen, Z. J. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 106:17835-17840.

Ha, M., Kim, E.-D., and Chen, Z. J. (2009) Duplicate genes increase expression diversity in related species and allopolyploids. Proc. Natl. Acad. Sci. USA 106:2295-2300.