Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
PLoS Comput Biol. 2009 Mar;5(3):e1000326. doi: 10.1371/journal.pcbi.1000326. Epub 2009 Mar 20.

A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.

Author information

  • 1Center for Genomics & Systems Biology, New York University, Department of Biology, New York, New York, United States of America.

Abstract

As sessile organisms, plants must cope with multiple and combined variations of signals in their environment. However, very few reports have studied the genome-wide effects of systematic signal combinations on gene expression. Here, we evaluate a high level of signal integration, by modeling genome-wide expression patterns under a factorial combination of carbon (C), light (L), and nitrogen (N) as binary factors in two organs (O), roots and leaves. Signal management is different between C, N, and L and in shoots and roots. For example, L is the major factor controlling gene expression in leaves. However, in roots there is no obvious prominent signal, and signal interaction is stronger. The major signal interaction events detected genome wide in Arabidopsis roots are deciphered and summarized in a comprehensive conceptual model. Surprisingly, global analysis of gene expression in response to C, N, L, and O revealed that the number of genes controlled by a signal is proportional to the magnitude of the gene expression changes elicited by the signal. These results uncovered a strong constraining structure in plant cell signaling pathways, which prompted us to propose the existence of a "code" of signal integration.

PMID:
19300494
[PubMed - indexed for MEDLINE]
PMCID:
PMC2652106
Free PMC Article

Images from this publication.See all images (8)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Public Library of Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk