E-GEOD-43162 - Expression data from poplar roots under nitrogen limitation

Status
Released on 17 July 2013, last updated on 29 July 2013
Organism
Populus tremula x Populus alba
Samples (26)
Array (1)
Protocols (7)
Description
We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation. Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.
Experiment type
transcription profiling by array 
Contacts
Victor Busov <vbusov@mtu.edu>, Victor B Busov, Yordan S Yordanov
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-43162.idf.txt
Sample and data relationshipE-GEOD-43162.sdrf.txt
Raw data (1)E-GEOD-43162.raw.1.zip
Processed data (1)E-GEOD-43162.processed.1.zip
Array designA-AFFY-131.adf.txt
Links