Transcriptomics

Dataset Information

5

Hypocotyl and cotyledon transcriptome in Arabidopsis thaliana treated with 1 ppm ethylene and shade (low PAR, low blue and low R:FR)


ABSTRACT: Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth. 1 day old Arabidopsis seedlings were subjected to control, ethylene and shade conditions. Hypocotyl and cotyledon tissues were harvested at 1.5 h, 13.5 h and 25.5 h of treatment time respectively. Microarray hybridization was carried out with 3 biological replicates (collected over 3 independent experiments) of each sample using the Affymetrix Arabidopsis Gene 1.1 ST platform.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Rashmi Sasidharan   L A Voesenek  Kate St.Onge  Debatosh Das  Ronald Pierik 

PROVIDER: E-GEOD-83212 | ArrayExpress | 2016-06-10

SECONDARY ACCESSION(S): GSE83212PRJNA325269

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

1000-01-01 | S-EPMC6203721 | BioStudies
2016-01-01 | S-EPMC4849989 | BioStudies
2016-06-30 | E-GEOD-79881 | ArrayExpress
2016-01-01 | S-EPMC4770057 | BioStudies
2015-01-01 | S-EPMC4779058 | BioStudies
1000-01-01 | S-EPMC3355348 | BioStudies
2018-01-01 | S-EPMC5808342 | BioStudies
1000-01-01 | S-EPMC3830486 | BioStudies
2014-01-01 | S-EPMC4056540 | BioStudies
2019-01-01 | S-EPMC6530356 | BioStudies