title: A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule".
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biology, New York University, Center for Genomics and Systems Biology, New York 10003, USA. dcn208@nyu.edu
authors.forename: Damion
authors.initials: D
authors.lastname: Nero
authors.forename: Gabriel
authors.initials: G
authors.lastname: Krouk
authors.forename: Daniel
authors.initials: D
authors.lastname: Tranchina
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Coruzzi
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000187:drug effects*; D017343:Genes, Plant / Q000235:genetics; D006728:Hormones / Q000494:pharmacology*; D005810:Multigene Family; D009566:Nitrates / Q000494:pharmacology*; D010944:Plants / Q000187:drug effects / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D049490:Systems Biology
chemical_list: D006728:Hormones; D009566:Nitrates