A map of cell type-specific auxin responses

Bastiaan O R Bargmann, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, Jiří Friml, Dominique C. Bergmann, Mark Estelle, Kenneth D. Birnbaum

Research output: Contribution to journalArticle


In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.

Original languageEnglish (US)
Article number688
JournalMolecular systems biology
Issue number1
StatePublished - Jan 1 2013


  • Arabidopsis
  • development
  • root apical meristem
  • signaling gradient

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

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  • Cite this

    Bargmann, B. O. R., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., Choe, G., Friml, J., Bergmann, D. C., Estelle, M., & Birnbaum, K. D. (2013). A map of cell type-specific auxin responses. Molecular systems biology, 9(1), [688]. https://doi.org/10.1038/msb.2013.40