Establishing a Framework for the Ad/Abaxial Regulatory Network of Arabidopsis: Ascertaining Targets of Class III HOMEODOMAIN LEUCINE ZIPPER and KANADI Regulation

• Published in: The Plant cell 2013-09, Vol.25 (9), p.3228-3249
• Main Authors: Reinhart, Brenda J., Liu, Tie, Newell, Nicole R., Magnani, Enrico, Huang, Tengbo, Kerstetter, Randall, Michaels, Scott, Barton, M. Kathryn
• Format: Article
• Language: English
• Subjects: Apical meristems; Arabidopsis - anatomy & histology; Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Binding Sites; Body Patterning; Datasets; Down regulation; Gene Expression; Gene Expression Profiling; Gene expression regulation; Gene Expression Regulation, Plant; Gene Regulatory Networks - genetics; Genes; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Large-Scale Biology; LARGE-SCALE BIOLOGY ARTICLE; Meristem - anatomy & histology; Meristem - genetics; Meristem - growth & development; Meristem - metabolism; Models, Biological; Mutation; Oligonucleotide Array Sequence Analysis; Phenotype; Phylogeny; Plant cells; Plant Leaves - anatomy & histology; Plant Leaves - genetics; Plant Leaves - growth & development; Plant Leaves - metabolism; Plant Shoots - anatomy & histology; Plant Shoots - genetics; Plant Shoots - growth & development; Plant Shoots - metabolism; Plants, Genetically Modified; rev genes; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Up regulation
• ISSN: 1040-4651; 1532-298X
• DOI: 10.1105/tpc.113.111518

The broadly conserved Class III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) and KANADI transcription factors have opposing and transformational effects on polarity and growth in all tissues and stages of the plant's life. To obtain a comprehensive understanding of how these factors work, we have identified transcripts that change in response to induced HD-ZIPIII or KANADI function. Additional criteria used to identify high-confidence targets among this set were presence of an adjacent HD-ZIPIII binding site, expression enriched within a subdomain of the shoot apical meristem, mutant phenotype showing defect in polar leaf and/or meristem development, physical interaction between target gene product and HD-ZIPIII protein, opposite regulation by HD-ZIPIII and KANADI, and evolutionary conservation of the regulator-target relationship. We find that HD-ZIPIII and KANADI regulate tissue-specific transcription factors involved in subsidiary developmental decisions, nearly all major hormone pathways, and new actors (such as INDETERMINATE DOMAIN4) in the ad/abaxial regulatory network. Multiple feedback loops regulating HD-ZIPIII and KANADI are identified, as are mechanisms through which HD-ZIPIII and KANADI oppose each other. This work lays the foundation needed to understand the components, structure, and workings of the ad/abaxial regulatory network directing basic plant growth and development.