title: Gene network analysis of Arabidopsis thaliana flower development through dynamic gene perturbations.
abstract: Understanding how flowers develop from undifferentiated stem cells has occupied developmental biologists for decades. Key to unraveling this process is a detailed knowledge of the global regulatory hierarchies that control developmental transitions, cell differentiation and organ growth. These hierarchies may be deduced from gene perturbation experiments, which determine the effects on gene expression after specific disruption of a regulatory gene. Here, we tested experimental strategies for gene perturbation experiments during Arabidopsis thaliana flower development. We used artificial miRNAs (amiRNAs) to disrupt the functions of key floral regulators, and expressed them under the control of various inducible promoter systems that are widely used in the plant research community. To be able to perform genome-wide experiments with stage-specific resolution using the various inducible promoter systems for gene perturbation experiments, we also generated a series of floral induction systems that allow collection of hundreds of synchronized floral buds from a single plant. Based on our results, we propose strategies for performing dynamic gene perturbation experiments in flowers, and outline how they may be combined with versions of the floral induction system to dissect the gene regulatory network underlying flower development.
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Diarmuid S
authors.initials: DS
authors.lastname: Ó'Maoiléidigh
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Bennett
authors.initials: B
authors.lastname: Thomson
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Raganelli
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Samuel E
authors.initials: SE
authors.lastname: Wuest
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Patrick T
authors.initials: PT
authors.lastname: Ryan
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Kamila
authors.initials: K
authors.lastname: Kwaśniewska
authors.affiliation: UMR 5168, Université Grenoble Alpes, F-38041, Grenoble, France.|UMR 5168, Centre National de la Recherche Scientifique, F-38054, Grenoble, France.|Laboratoire Physiologie Cellulaire et Végétale, Comissariat a l'Energie Atomique (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), F-38054, Grenoble, France.|Institut National de la Recherche Agronomique, F-38054, Grenoble, France.
authors.forename: Cristel C
authors.initials: CC
authors.lastname: Carles
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.|Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Graciet
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Frank
authors.initials: F
authors.lastname: Wellmer
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development*; D035264:Flowers / Q000254:growth & development*; D055785:Gene Knockdown Techniques; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D008969:Molecular Sequence Data; D018749:RNA, Plant / Q000235:genetics
chemical_list: D018749:RNA, Plant
keywords: Arabidopsis thaliana; artificial miRNAs; flower development; gene perturbation; gene regulatory network; inducible promoter systems; technical advance