E-GEOD-45806 - transcriptome analysis of differentially expressed genes in the harlequin (hlq) mutant

Status
Released on 3 June 2014, last updated on 7 June 2014
Organism
Arabidopsis thaliana
Samples (8)
Array (1)
Protocols (10)
Description
Plant growth and development is continuous and modular, a combination that allows morphogenesis by controlled cell division and elongation and serves to facilitate plants’ adaptations to changing environments. Plasticity is achieved through integration of external and internal signals to regulate meristem activities. We previously characterized the pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of ABA- and auxin-inducible proDc3:GUS in roots and hypocotyls. Mutants are skotomorphogenic (dark development of true leaves and chlorophyll accumulation), have deformed and collapsed epidermal cells that accumulate callose and starch and stain strongly with the vital dye fluorescein diacetate, brittle stems and leaves, cell walls with a relative abundance of pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes. We cloned hlq and show it is an allele of brassinosteroid-insensitive3/hypocotyl6/root hairless3/Topoisomerase6B. Mutants affecting the cell wall and inhibitors of cellulose synthesis and N-glycosylation phenocopy several of the traits of hlq such as ectopic proDc3:GUS expression, lignin accumulation, and bulging root tips and epidermal cells. We performed a microarray analysis of genes differentially expressed in hlq mutants and observed coordinated expression of adjacent pairs/sets of genes suggesting a direct effect on chromatin remodeling, and significantly mis-regulated genes for histones, WRKY and IAA/AUX transcription factors, aquaporins, ubiquin E3-ligase mediated proteolysis and autophagy, biotic stress response markers, as well as numerous other cellular and metabolic processes affecting carbon partitioning into secondary metabolites lignin and anthocyanin. Our results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodeling that mediates cell wall metabolism, growth, and development in response to environmental and hormonal signals. Seven samples; four mutant, three wild type in a dual color competitive hybridization to four microarray slides. One 'quasi-technical' replicate slide made up of pools of the three biological replicates plus a fourth mutant replicate.
Experiment type
transcription profiling by array 
Contacts
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-45806.idf.txt
Sample and data relationshipE-GEOD-45806.sdrf.txt
Raw data (1)E-GEOD-45806.raw.1.zip
Processed data (1)E-GEOD-45806.processed.1.zip
Array designA-GEOD-16970.adf.txt
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