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Research Interests
- Transcriptional control of salt stress responses in roots
- Root development
- Systems biology
Research Overview
Our lab focuses on understanding how developmental processes such as cell-type specification regulate responses to environmental change. Environmental stimuli have been used as powerful tools for dissecting fundamental processes in biology. In single-celled organisms such as yeast, pioneering work has led to a deep understanding as to how gene expression is regulated. In multicellular organisms, similar approaches have been taken, however most of these studies assume that the various cell-types composing an organism respond to stimuli similarly.
We have recently shown that developmental parameters play a key role in determining the transcriptional response of cells to high salinity. Using Fluorescence Activated Cell Sorting (FACS) to isolate cells from roots expressing Green Fluorescent Protein (GFP) in specific cell types, we were able to generate a high resolution gene expression map. This map details the expression pattern of over 23,000 Arabidopsis genes in roots grown under both standard and high salinity conditions. With this expression map, we have shown that previously characterized pathways that control salt stress responses appear to primarily regulate transcriptional events occurring in multiple cell-types. Cell-type specific transcriptional responses, which constitute the bulk of the response, are controlled by unknown mechanisms. Identifying and characterizing these mechanisms will be at the heart of the Dinneny lab’s research. This work will lead to a deep understanding of how a multicellular organ responds and potentially adapts to environmental change and will break new ground connecting upstream developmental pathways to downstream physiology
Cis-element code
One of the primary projects of the lab will be to decipher the “cis-element code” controlling the activity of cell-type specific salt responsive promoters. In collaboration with Uwe Ohler at the Institute for Genome Sciences and Policy at Duke University, we are developing a computational algorithm to identify DNA sequence motifs associated with genes regulated by salt stress in specific cell layers of the root. We will then directly test the function of these putative cis-elements in reporter-based assays.
Spatio-temporal analysis of salt stress
While our salt-stress root expression map represents the highest resolution view that we have of how a multicellular organ responds to an external stimulus, it is unclear how the transcriptional changes we observe relate to long-term changes that may be important for adaptation. In our previous study, we examined the salt stress response after one hour of treatment. Now, we will expand our expression map in time to examine how the various cell layers respond to salt over longer periods of high salinity. This spatio-temporal response map may also be useful for characterizing inter-cell layer communication important for the salt-stress response.
Developmental control of physiological responses to stress
Work on cell-type specification pathways in Arabidopsis has identified many transcription factors that are necessary to generate the various cell layers of the root. Previously, we have shown that disruption of cell-fate specification leads to autonomous and non-autonomous effects on salt responses in the root, however, little is known as to how this occurs. To elucidate the nature of this regulation, we will begin to characterize the downstream targets of known cell-identity regulators in the root, which are involved in the salt stress response. This work will have the long-term objective of understanding how upstream processes such as cell-type specification eventually regulate the nature of a cell’s response to the external environment.
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