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Regulation of Gene Expression during Plant Embryogenesis
Department of Plant and Soil Sciences
Somatic embryogenesis is a poorly understood process that is of value to agriculture because a means of regeneration, either by organogenesis or somatic embryogenesis, is necessary for genetic engineering for crop improvement of most plants. AGL15 is a protein that controls expression of genes, is most abundant during embryo development, and can promote somatic embryogenesis. The proposed work to identify genes directly and indirectly controlled by AGL15 will contribute to a better understanding of genetic processes controlling zygotic and somatic embryo development.
2009 Project Description
We have continued to probe mechanisms underpinning plant embryogenesis by identifying genes directly and indirectly regulated by the DNA-binding MADS-factor AGL15. AGL15 accumulation correlates with competence for somatic embryogenesis. Understanding somatic embryo development is fascinating from the basic viewpoint of determining how a cell can dedifferentiate and redifferentiate in embryo mode, as well as having practical aspects to promote regeneration of value-added transgenic plants by somatic embryogenesis.
One route to contribute to determination of mechanisms of somatic embryo development is to determine genes controlled by transcriptional regulators that promote this process, such as AGL15. We have globally mapped where AGL15 associates with DNA in vivo, resulting in ~2000 binding sites. We have combined this information with expression microarray data to determine perturbations in the transcriptome in response to increased or decreased AGL15. This has allowed us to identify genes that are likely to be directly expressed in response to AGL15 as well as genes directly repressed by AGL15, resulting in ~200 genes with a direct, consistent and significant response to AGL15. Interestingly, other transcriptional regulators are overrepresented in the directly expressed list, but not the directly repressed list. DNA motifs that AGL15 recognizes are overrepresented in the fragments identified as bound by AGL15. We published this work in The Plant Cell in 2009.
Currently we are focusing on objectives 3 and 4 of the project to confirm direct targets as regulated by AGL15 (and the redundant AGL18) and to determine the function of regulated genes.
Finally we are developing tools to allow us to extend the gene regulation network underlying embryogenesis by looking at genes regulated by some AGL15 targets that encode transcriptional regulators. The data obtained has also led to collaborations resulting in a publication in the Journal of Experimental Botany in 2009 and an ongoing collaboration with a researcher at the University of Wisconsin-Madison.
Limited number of studies have been performed to globally identify direct targets of plant transcription factors. Consequently not much is known about the number or types of targets that a specific factor controls.
We have now published our results adding to an emerging picture of transcriptional control. We have found, as have others, that while many sites are occupied by a given transcription factor in vivo (generally 1000s of DNA binding sites), relatively few interactions between a transcriptional regulator and DNA result in significant changes in gene expression of the nearby gene. There are numerous possible reasons, but it seems important to assess the impact of DNA-protein interaction.
Analysis of genes directly and indirectly controlled by AGL15 has led us to investigate hormone interactions involved in control of somatic embryo development. We are currently using combinations of mutants, hormones and inhibitor treatments to tease apart how different hormones cross-talk in control of somatic embryo development. We have extended our work in Arabidopsis and demonstrated that ectopic expression of AGL15 in soybean can promote somatic embryogenesis in this important crop.
Zheng, Y., Ren, N., Wang, H., Stromberg, A.J. and Perry, S.E. 2009. Global Identification of Targets of the Arabidopsis MADS Domain Protein AGAMOUS-Like15. The Plant Cell 21, 2563-2577.
Nakaminami, K., Hill, K., Perry, S.E., Sentoku, N., Long, J.A. and Karlson, D.T. 2009. Arabidopsis Cold Shock Domain Proteins: Relationships to Floral and Silique Development. Journal of Experimental Botany 60, 1047-1062.