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Series GSE45806 Query DataSets for GSE45806
Status Public on Jun 03, 2014
Title transcriptome analysis of differentially expressed genes in the harlequin (hlq) mutant
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary 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.
Overall design 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.
Contributor(s) Rock CD
Citation(s) 24821950
Submission date Apr 05, 2013
Last update date Jun 04, 2014
Contact name Christopher Dale Rock
Phone (806) 742-2715
Organization name Texas Tech University
Department Biological Sciences
Lab mailstop 3131
Street address Flint and Main Sts.
City Lubbock
State/province TX
ZIP/Postal code 79409-3131
Country USA
Platforms (1)
GPL16970 Galbraith Laboratory Operon Long Oligonucleotide Microarray version 3.0 (ATv3.6.1.Z)
Samples (4)
GSM1115795 wild type_rep1 vs. hlq mutant_rep1
GSM1115796 hlq mutant_rep2_vs wild type_rep2
GSM1115797 wild type_rep3 vs. hlq_rep3
BioProject PRJNA196405

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45806_RAW.tar 16.5 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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