Transcriptomics

Dataset Information

38

Transcriptome analysis of differentially expressed genes in the harlequin (hlq) mutant


ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Christopher D Rock  Christopher Dale Rock    

PROVIDER: E-GEOD-45806 | ArrayExpress | 2014-06-07

SECONDARY ACCESSION(S): GSE45806PRJNA196405

REPOSITORIES: GEO, ArrayExpress

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Publications

TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis.

Mittal Amandeep A   Balasubramanian Rajagopal R   Cao Jin J   Singh Prabhjeet P   Subramanian Senthil S   Hicks Glenn G   Nothnagel Eugene A EA   Abidi Noureddine N   Janda Jaroslav J   Galbraith David W DW   Rock Christopher D CD  

Journal of experimental botany 20140512 15


Plant growth is continuous and modular, a combination that allows morphogenesis by cell division and elongation and serves to facilitate adaptation to changing environments. The pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of the abscisic acid (ABA)- and auxin-inducible proDc3:GUS reporter gene, were previously characterized. Mutants are skotomorphogenic, have deformed and collapsed epidermal cells which accumulate callose and starch, cell wal  ...[more]

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