Our mission: to understand the mechanisms governing the response of plants to environmental change

Cells must constantly assess current environmental conditions and generate an output that is contextually appropriate. The elegantly simple organization of the root provides a unique opportunity to explore these processes in a multi-cellular organ with the goal of discovering fundamental principles of signal integration that also apply to other biological systems. Our research is aimed at understanding four questions:

• How does spatial and temporal information regulate the response and acclimation of the root to high salinity?

• How does information encoded in the promoter enable a gene to be environmentally responsive?

• What is the role of developmental pathways in regulating salt-stress responses?

• What is the role of local perception in environmental response?

Salinity research in the Dinneny lab


Our lab focuses on understanding how developmental processes such as cell-type specification regulate responses to environmental change. While understanding the mechanisms controlling environmental response is a major focus in plant biology, most studies have considered the organ or even the whole organism as a single responsive unit and ignore the potential diversity of responses that may be afforded by the various cell-types composing an organism. We have shown that developmental parameters play a key role in determining the transcriptional response of cells to high salinity.

In Previous work we used Fluorescence Activated Cell Sorting to isolate specific cell-types from roots, we were able to generate a high-resolution gene expression map (Dinneny et al., 2008). 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 regulatory pathways primarily control transcriptional events occurring in multiple cell-types while cell-type specific responses, which constitute the bulk of the response, are controlled by unknown mechanisms. Identifying and characterizing these unknown mechanisms is at the heart of our current 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.

Deciphering the cis-regulatory code controlling cell-type specific responses to salt stress

Understanding the mechanisms controlling gene expression patterns remains a central question in biology. While many studies begin and end with the characterization of a single cis-regulatory element, the goal of our current work is to develop a comprehensive understanding of the many different sequences that contribute to the salt-stress response. As the cost of gene synthesis has fallen, we have devised a synthetic biology approach to cis- element analysis. We are constructing synthetic regulatory regions containing predicted cis- element sequences identified using various computational algorithms (FIRE, cERMIT, Athena). We are generating synthetic regulatory regions for these putative elements and will test whether these sequences are sufficient to drive spatial or environmentally regulated expression patterns in the root.

Novel cis-elements found to be important will provide a valuable resource for identifying the associated TFs. Our synthetic promoters provide ideal baits in yeast-1-hybrid screens to identify the associated TFs. These data will be used to generate a cis-element centered transcriptional networks, which will aid in understanding how complex patterns of expression are generated during environmental stress. This project is in collaboration with Steve Kay and José Pruneda-Paz at the University of California, San Diego.

Understanding the mechanisms governing "hydropatterning" in roots

Fresh water constitutes less than 1% of the surface water on earth, yet the importance of this simple molecule to all life forms is immeasurable. Water represents the most vital reagent for chemical reactions occurring in a cell. In plants, water provides the structural support necessary for plant growth. It acts as the carrier for nutrients absorbed from the soil and transported to the shoot. It also provides the chemical components necessary to generate sugar and biomass from light and carbon dioxide during photosynthesis. While the importance of water to plants is clear, an understanding as to how plants perceive water is limited. Most studies have focused on environmental conditions in which severe limitation (drought) or severe excess (flooding) of water is simulated. While these are important stress conditions, the plant may also sense and respond to differences in moisture content under non-stress conditions. Much as how light can act as a signal or a stress depending on the intensity, water may also have such a dual effect. In support of this hypothesis, work on hydrotropism has shown that roots have the ability to sense moisture gradients and direct growth towards favorable conditions.

Our current studies indicate that moisture signaling may extend beyond hydrotropism and regulate nearly every aspect of root development. In a process we term "hydropatterning", local contact of the root tip with a liquid or air environment has the ability to cause stark differences in the development of tissues. Hydropatterning is observed in Arabidopsis thaliana as well as other flowering plants. The goal of our current research is to establish a foundation for understanding hydropatterning by characterizing the changes in growth and development that are directly affected. Using developmental and cell-type specific approaches along with genetic and genomic tools, our research will identify the key pathways through which moisture signaling acts to affect these processes.


Emami, S, Yee MC, Dinneny JR (2013) A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Front. Plant Sci. 4:339. doi: 10.3389/fpls.2013.00339

Geng Y, Wu R, Wee CW, Xie F, Wei X, Chan PMY, Tham C, Duan L, Dinneny JR (2013) A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis. The Plant Cell doi:10.1105/tpc.113.112896

Duan L, Dietrich D, Ng CH, Chan PMY, Bhalerao R, Bennett MJ, Dinneny JR (2013) Endodermal ABA signaling promotes lateral root quiescence during salt stress in Arabidopsis thaliana seedlings. The Plant Cell PMID: 23341337

Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN (2009) Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods in Molecular Biology 553:57-77

Dinneny JR, Long TA, Wang JY, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein, JS, Benfey PN (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science May 16;320(5878):942-5

Filiault D, Wessinger C, Dinneny JR, Lutes J, Borevitz J, Weigel D, Chory J, and Maloof JN (2008) Amino acid polymorphisms in Arabidopsis Phytochrome B causes differential response to light. Proc. Natl. Acad. Sci. Feb 26;105(8):3157-62

Brady SM, Orlando D, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science Nov 2;318(5851):801-6

Dinneny JR, Weigel D, Yanofsky MF (2006) NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis. Development 133, 1645-1655

Dinneny JR, Weigel D, Yanofsky MF (2005) A genetic framework for fruit patterning in Arabidopsis. Development 132, 4687-4696

Dinneny JR, Yadegari R, Fischer RL, Yanofsky MF, Weigel D (2004) The role of JAGGED in shaping lateral organs. Development 131, 1101-1110
(‘Previews’ in Developmental Cell 6(3), 318-319)

Wu X, Dinneny JR, Crawford KM, Rhee Y, Citovsky V, Zambryski PC, Weigel D (2003) Modes of intercellular transcription factor movement in the Arabidopsis apex. Development 130, 3735-3745.

Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny J, Wells D, Katz A, Margossian L, Harada J, Goldberg R, Fischer RL (1999) Control of fertilization-independent-endosperm development by the MEDEA polycomb gene in Arabidopsis. Proc. Natl. Acad. Sci. 96, 4186-4191.

Reviews and Book Chapters
Dinneny JR (2012) Cell-type resolution analysis of root development and environmental responses. Roots and their soil interactions: What we can learn from genomics. Wiley Publishing

Wee CW and Dinneny JR (2010) Tools for high-spatial and temporal-resolution analysis of environmental responses in plants. Biotechnology Letters PMID: 20502944

Dinneny JR (2010) Analysis of the salt-stress response at cell-type resolution. Plant Cell & Environment 1;33(4):543-51

Dinneny JR, Benfey PN (2009) Studying root development using a genomic approach. Annual Plant Reviews, Volume 37, Root Development Chapter 12: 325-351 Blackwell Publishing

Dinneny JR and Benfey PN (2008) Plant stem cell niches: standing the test of time. Cell Feb 22;132(4):553-7

Dinneny JR and Benfey PN, (2005) Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development. Cell 123, 1180-1182

Dinneny JR and Yanofsky MF (2005) Drawing lines and borders: how the dehiscent fruit of Arabidopsis is patterned. Bioessays 27, 42-49

Dinneny JR and Yanofsky MF (2004) Floral Development: An ABC Gene Chips in Downstream. Curr. Biol. 14, R840-R841

Dinneny JR and Yanofsky MF (2004) Vascular Patterning: Xylem or Phloem? Curr. Biol. 14, R112-R114

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