Genome-wide Identification of KANADI1 Target Genes

PLoS One. 2013 Oct 14;8(10):e77341. doi: 10.1371/journal.pone.0077341. eCollection 2013.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / drug effects
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Base Sequence
  • Chromatin Immunoprecipitation
  • Gene Expression Regulation, Plant / drug effects
  • Gene Ontology
  • Genes, Plant / genetics*
  • Homeodomain Proteins / metabolism
  • Indoleacetic Acids / pharmacology
  • Molecular Sequence Data
  • Organogenesis / drug effects
  • Organogenesis / genetics
  • Promoter Regions, Genetic / genetics
  • Protein Binding / drug effects
  • Protein Binding / genetics
  • Sequence Analysis, DNA
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription, Genetic / drug effects

Substances

  • Arabidopsis Proteins
  • Homeodomain Proteins
  • IFL1 protein, Arabidopsis
  • Indoleacetic Acids
  • KANADI protein, Arabidopsis
  • Transcription Factors

Grant support

MH acknowledges the Australian Research Council (http://www.arc.gov.au/) and European Research Council (GA Nº261081)(http://erc.europa.eu/) for current funding. The SW laboratory is funded by grants of the Deutsche Forschungsgemeinschaft (WE4281/6-1, WE4281/7-1) (http://www.dfg.de/) and the European Union (FP7 No. 256502) (http://cordis.europa.eu/fp7/home_en.html). LB was supported by the Swiss national Science Foundation (PBZHA-1188060)(http://www.snf.ch/E/Pages/default.aspx) and JLB acknowledges support from the Australian Research Council (DP0771232, DP110100070)(http://www.arc.gov.au/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.