Genome‐wide binding‐site analysis of REVOLUTA reveals a link between leaf patterning and light‐mediated growth responses

• Published in: The Plant journal : for cell and molecular biology Vol. 72; no. 1; pp. 31 - 42
• Main Authors: Brandt, Ronny, Salla‐Martret, Mercè, Bou‐Torrent, Jordi, Musielak, Thomas, Stahl, Mark, Lanz, Christa, Ott, Felix, Schmid, Markus, Greb, Thomas, Schwarz, Martina, Choi, Sang‐Bong, Barton, M. Kathryn, Reinhart, Brenda J, Liu, Tie, Quint, Marcel, Palauqui, Jean‐Christophe, Martínez‐García, Jaime F, Wenkel, Stephan
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.10.2012; Blackwell; Wiley
• Subjects: Adaptation, Physiological; Agricultural sciences; animals; Arabidopsis; Arabidopsis - cytology; Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - radiation effects; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; auxin; auxins; Binding Sites; Biological and medical sciences; Biosynthesis; Body Patterning; Cell differentiation, maturation, development, hematopoiesis; Cell physiology; Chromatin Immunoprecipitation; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; genes; Genome, Plant - genetics; Genomics; HD‐ZIPII; HD‐ZIPIII; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Hypocotyl - cytology; Hypocotyl - genetics; Hypocotyl - growth & development; Hypocotyl - radiation effects; In Situ Hybridization; Indoleacetic Acids - analysis; Indoleacetic Acids - metabolism; leaf development; leaves; leucine zipper; Life Sciences; Light; Molecular and cellular biology; Morphology; Mutation; Phylogeny; Plant biology; Plant growth; Plant Leaves - cytology; Plant Leaves - genetics; Plant Leaves - growth & development; Plant Leaves - radiation effects; plant morphology; Plant physiology and development; proteins; sequence analysis; Sequence Analysis, DNA; shade avoidance; shoots; Signal Transduction; transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; vegetative growth; Patterning; Auxin; Growth; Plant leaf; Binding site; HD-ZIPII; Arabidopsis thaliana; shade avoidance; Cruciferae; Dicotyledones; Light; Angiospermae; Development; Plant growth substance; Spermatophyta; HD-ZIPIII; Avoidance; leaf development; ZIP; auxin; POLARITY; TRANSCRIPTION; PLANT DEVELOPMENT; CELL FATE; REGULATOR; SHADE-AVOIDANCE RESPONSES; GENE; AUXIN BIOSYNTHESIS; ARABIDOPSIS
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/j.1365-313X.2012.05049.x

Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD‐ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD‐ZIPIII proteins control several polarity set‐up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD‐ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP‐Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD‐ZIP transcription factors that have been shown to act in the shade‐avoidance response pathway. We show that, as well as involvement in basic patterning, HD‐ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD‐ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD‐ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.