NDLI: Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis

Content Provider	Springer Nature : BioMed Central
Author	Gutiérrez, Rodrigo A Lejay, Laurence V Dean, Alexis Chiaromonte, Francesca Shasha, Dennis E Coruzzi, Gloria M
Abstract	Background Carbon (C) and nitrogen (N) metabolites can regulate gene expression in Arabidopsis thaliana. Here, we use multinetwork analysis of microarray data to identify molecular networks regulated by C and N in the Arabidopsis root system. Results We used the Arabidopsis whole genome Affymetrix gene chip to explore global gene expression responses in plants exposed transiently to a matrix of C and N treatments. We used ANOVA analysis to define quantitative models of regulation for all detected genes. Our results suggest that about half of the Arabidopsis transcriptome is regulated by C, N or CN interactions. We found ample evidence for interactions between C and N that include genes involved in metabolic pathways, protein degradation and auxin signaling. To provide a global, yet detailed, view of how the cell molecular network is adjusted in response to the CN treatments, we constructed a qualitative multinetwork model of the Arabidopsis metabolic and regulatory molecular network, including 6,176 genes, 1,459 metabolites and 230,900 interactions among them. We integrated the quantitative models of CN gene regulation with the wiring diagram in the multinetwork, and identified specific interacting genes in biological modules that respond to C, N or CN treatments. Conclusion Our results indicate that CN regulation occurs at multiple levels, including potential post-transcriptional control by microRNAs. The network analysis of our systematic dataset of CN treatments indicates that CN sensing is a mechanism that coordinates the global and coordinated regulation of specific sets of molecular machines in the plant cell.
Related Links	https://genomebiology.biomedcentral.com/counter/pdf/10.1186/gb-2007-8-1-r7.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/gb-2007-8-1-r7
Journal	Genome Biology
Issue Number	1
Volume Number	8
Language	English
Publisher	BioMed Central
Publisher Date	2007-01-11
Access Restriction	Open
Subject Keyword	Animal Genetics and Genomics Human Genetics Plant Genetics and Genomics Microbial Genetics and Genomics Bioinformatics Evolutionary Biology Additional Data File Arabidopsis Root Molecular Machine Auxin Efflux Carrier Affymetrix Gene Chip
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	10.1/2023
5-Year Journal Impact Factor	16.5/2023

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Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis

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