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2013;8 (10): e77341.

Genome-wide identification of KANADI1 target genes.

Paz Merelo, Yakun Xie, Lucas Brand, Felix Ott, Detlef Weigel, John L Bowman, Marcus G Heisler, Stephan Wenkel
Author Information
  1. Paz Merelo: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
PMID: 24155946 DOI: 10.1371/journal.pone.0077341

Abstract

Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.

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MeSH Term

Arabidopsis
Arabidopsis Proteins
Base Sequence
Chromatin Immunoprecipitation
Gene Expression Regulation, Plant
Gene Ontology
Genes, Plant
Homeodomain Proteins
Indoleacetic Acids
Molecular Sequence Data
Organogenesis
Promoter Regions, Genetic
Protein Binding
Sequence Analysis, DNA
Transcription Factors
Transcription, Genetic

Chemicals

Arabidopsis Proteins
Homeodomain Proteins
IFL1 protein, Arabidopsis
Indoleacetic Acids
KANADI protein, Arabidopsis
Transcription Factors
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

Created with Highcharts 10.0.0genesorganKAN1developmenttargetpolarityregulationestablishmentseveraltranscriptionfactorsfamilyimportantpatterninginvolvedresponseauxinshownalsoacidPlantmediatedactionAmongKANADIKANsubcladeGARPproteinplaysrolespolarity-associatedprocessesembryoshootrootstudyidentifiedsetpotentialdirectcombinationchromatinimmunoprecipitation/DNAsequencingChIP-Seqgenome-widetranscriptionalprofilingusingtilingarraysTargetover-representedwellaffectsdirectlyexpressionpreviouslylateralvasculartissueshowcontrolseffectsdifferentlevels:transportsignalingadditionregulatesabscisicjasmonicbrassinosteroidsethylenecytokininsgibberellinsroleantagonizedHD-ZIPIIIincludingREVOLUTAREVcomparisonrevealsREV/KAN1moduleactsoppositesharedtargetsEvidencemutualrepressioncloselyrelatedmembersGenome-wideidentificationKANADI1

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