Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

Gabriel Krouk, Piotr Mirowski, Yann LeCun, Dennis Shasha, Gloria Coruzzi

Research output: Contribution to journalArticle

Abstract

Background: Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified.Results: Here we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes and functions needed to prepare plants to use or reduce nitrate. A state-space model inferred from this microarray time-series data successfully predicts gene behavior in unlearnt conditions.Conclusions: The experiments and methods allow us to propose a temporal working model for nitrate-driven gene networks. This network model is tested both in silico and experimentally. For example, the over-expression of a predicted gene hub encoding a transcription factor induced early in the cascade indeed leads to the modification of the kinetic nitrate response of sentinel genes such as NIR, NIA2, and NRT1.1, and several other transcription factors. The potential nitrate/hormone connections implicated by this time-series data are also evaluated.

Original languageEnglish (US)
Article numberR123
JournalGenome Biology
Volume11
Issue number12
DOIs
StatePublished - Dec 23 2010

Fingerprint

Transcriptome
transcriptome
Nitrates
nitrates
nitrate
gene
modeling
time series analysis
Gene Regulatory Networks
Genes
time series
genes
Transcription Factors
transcription factors
Space Simulation
Plant Development
plant adaptation
Oligonucleotide Array Sequence Analysis
Arabidopsis
Computer Simulation

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. / Krouk, Gabriel; Mirowski, Piotr; LeCun, Yann; Shasha, Dennis; Coruzzi, Gloria.

In: Genome Biology, Vol. 11, No. 12, R123, 23.12.2010.

Research output: Contribution to journalArticle

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