title: Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.
abstract: In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana PIFs initiate transcriptional reprogramming in both organs within 15 min, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs.
authors.affiliation: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Markus V
authors.identifier: 0000-0001-5075-575X
authors.initials: MV
authors.lastname: Kohnen
authors.affiliation: SIB Swiss Institute of Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Emanuel
authors.identifier: 0000-0003-1339-5120
authors.initials: E
authors.lastname: Schmid-Siegert
authors.affiliation: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Martine
authors.initials: M
authors.lastname: Trevisan
authors.affiliation: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Laure Allenbach
authors.initials: LA
authors.lastname: Petrolati
authors.affiliation: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Fabien
authors.identifier: 0000-0002-4145-7205
authors.initials: F
authors.lastname: Sénéchal
authors.affiliation: Section of Plant Biology, Division of Biological Sciences, University of California, Davis, California 95616.
authors.forename: Patricia
authors.identifier: 0000-0001-9237-1797
authors.initials: P
authors.lastname: Müller-Moulé
authors.affiliation: Section of Plant Biology, Division of Biological Sciences, University of California, Davis, California 95616.
authors.forename: Julin
authors.identifier: 0000-0002-9623-2599
authors.initials: J
authors.lastname: Maloof
authors.affiliation: SIB Swiss Institute of Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Ioannis
authors.identifier: 0000-0002-3413-6841
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland christian.fankhauser@unil.ch.
authors.forename: Christian
authors.identifier: 0000-0003-4719-5901
authors.initials: C
authors.lastname: Fankhauser
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D018548:Cotyledon / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins