A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"

Damion Nero, Gabriel Krouk, Daniel Tranchina, Gloria M. Coruzzi

Research output: Contribution to journalArticle

Abstract

Background: Nitrate-induced reprogramming of the transcriptome has recently been shown to be highly context dependent. Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO3-signaling. Results: Biclustering was used to identify a set of genes that are N-responsive across a range of Nitrogen (N)-treatment backgrounds (i.e. nitrogen treatments under different growth conditions) using a meta-dataset of 76 Affymetrix ATH1 chips from 5 different laboratories. Twenty-one biclusters were found to be N-responsive across subsets of this meta-dataset. N-bicluster 9 (126 genes) was selected for further analysis, as it was shown to be reproducibly responsive to NO3 -as a signal, across a wide-variety of background conditions and datasets. N-bicluster 9 genes were then used as "seed" to identify putative cross-talk mechanisms between nitrate and hormone signaling. For this, the 126 nitrate-regulated genes in N-bicluster 9 were biclustered over a meta-dataset of 278 ATH1 chips spanning a variety of hormone treatments. This analysis divided the bicluster 9 genes into two classes: i) genes controlled by NO3-only vs. ii) genes controlled by both NO3-and hormones. The genes in the latter group showed a NO3-response that is significantly enhanced, compared to the former. In silico analysis identified two Cis-Regulatory Elements candidates (CRE) (E2F, HSE) potentially involved the interplay between NO3- and hormonal signals. Conclusion: This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development.

Original languageEnglish (US)
Article number59
JournalBMC Systems Biology
Volume3
DOIs
StatePublished - Jun 6 2009

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Systems Biology
Nitrate
Nitrates
Genes
Hormones
Gene
Crosstalk
Nitrogen
Chip
Biclustering
Plant Development
Systems Analysis
Growth Conditions
Transcriptome
Computer Simulation
Seed
Seeds
Likely
Systems analysis
Subset

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology
  • Computer Science Applications
  • Applied Mathematics
  • Modeling and Simulation

Cite this

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abstract = "Background: Nitrate-induced reprogramming of the transcriptome has recently been shown to be highly context dependent. Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO3-signaling. Results: Biclustering was used to identify a set of genes that are N-responsive across a range of Nitrogen (N)-treatment backgrounds (i.e. nitrogen treatments under different growth conditions) using a meta-dataset of 76 Affymetrix ATH1 chips from 5 different laboratories. Twenty-one biclusters were found to be N-responsive across subsets of this meta-dataset. N-bicluster 9 (126 genes) was selected for further analysis, as it was shown to be reproducibly responsive to NO3 -as a signal, across a wide-variety of background conditions and datasets. N-bicluster 9 genes were then used as {"}seed{"} to identify putative cross-talk mechanisms between nitrate and hormone signaling. For this, the 126 nitrate-regulated genes in N-bicluster 9 were biclustered over a meta-dataset of 278 ATH1 chips spanning a variety of hormone treatments. This analysis divided the bicluster 9 genes into two classes: i) genes controlled by NO3-only vs. ii) genes controlled by both NO3-and hormones. The genes in the latter group showed a NO3-response that is significantly enhanced, compared to the former. In silico analysis identified two Cis-Regulatory Elements candidates (CRE) (E2F, HSE) potentially involved the interplay between NO3- and hormonal signals. Conclusion: This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development.",
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