Research Lab Members:
Fang, Lei
Guan, Xueying
Huang, Tien-Yu
Ko, Dae Kwan
Lu, Jie
Miller, Marisa
Ng, Danny
Park, Gyoungju N.
Shi, Xiaoli
Zhang, Changqing
Research Summary:
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.
Publications:
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2012
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Lu, J., Zhang, C., Baulcombe, D. C., and Chen, Z. J. ,
Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds,
Proc. Natl. Acad. Sci. USA
109:
5529-5534
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2011
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Ha, M., Ng, D. W.-K., Li, W.-H., and Chen, Z. J.,
Coordinated histone modifications are associated with gene expression variation within and between species,
Genome Research
21:
590-598
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2011
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Ng, D. W., Zhang, C., Miller, M., Palmer, G., Whiteley, M., Tholl, D., and Chen, Z. J.,
Cis- and trans-regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids,
Plant Cell
23:
1729-1740
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2010
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Chen, Z. J.,
Molecular mechanisms of polyploidy and hybrid vigor,
Trends in Plant Science
15:
57-71
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2009
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Pang, M., Woodward, A. W., Agarwal, V., Ha, M., Guan, X., Vanitharani Ramachandran, V., Chen, X., Triplett, B. A., Stelly, D. M., and Chen, Z. J.,
Genome-wide analysis revealed rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.),
Genome Biology
10:
R122
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2009
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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.,
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids,
Proc. Natl. Acad. Sci. USA
106:
17835-17840
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2009
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Ni, Z., Kim, E., Ha, M., Lackey, E., Liu, J., Zhang, Y., Sun, Q., and Chen, Z. J.,
Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids,
Nature
457:
327-331
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2007
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Chen, Z. J.,
Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids,
Annual Review in Plant Biology
58:
377-406
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