title: Inference of the Arabidopsis lateral root gene regulatory network suggests a bifurcation mechanism that defines primordia flanking and central zones.
abstract: A large number of genes involved in lateral root (LR) organogenesis have been identified over the last decade using forward and reverse genetic approaches in Arabidopsis thaliana. Nevertheless, how these genes interact to form a LR regulatory network largely remains to be elucidated. In this study, we developed a time-delay correlation algorithm (TDCor) to infer the gene regulatory network (GRN) controlling LR primordium initiation and patterning in Arabidopsis from a time-series transcriptomic data set. The predicted network topology links the very early-activated genes involved in LR initiation to later expressed cell identity markers through a multistep genetic cascade exhibiting both positive and negative feedback loops. The predictions were tested for the key transcriptional regulator AUXIN RESPONSE FACTOR7 node, and over 70% of its targets were validated experimentally. Intriguingly, the predicted GRN revealed a mutual inhibition between the ARF7 and ARF5 modules that would control an early bifurcation between two cell fates. Analyses of the expression pattern of ARF7 and ARF5 targets suggest that this patterning mechanism controls flanking and central zone specification in Arabidopsis LR primordia.
authors.affiliation: Institut de Recherche pour le Développement, UMR DIADE, 34394 Montpellier cedex 5, France Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom.
authors.forename: Julien
authors.initials: J
authors.lastname: Lavenus
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan.
authors.forename: Tatsuaki
authors.initials: T
authors.lastname: Goh
authors.affiliation: Université de Montpellier, UMR DIADE, 34394 Montpellier cedex 5, France.
authors.forename: Soazig
authors.initials: S
authors.lastname: Guyomarc'h
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom.
authors.forename: Kristine
authors.initials: K
authors.lastname: Hill
authors.affiliation: Institut de Recherche pour le Développement, UMR DIADE, 34394 Montpellier cedex 5, France.
authors.forename: Mikael
authors.initials: M
authors.lastname: Lucas
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom.
authors.forename: Ute
authors.initials: U
authors.lastname: Voß
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom.
authors.forename: Kim
authors.initials: K
authors.lastname: Kenobi
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Wilson
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom Inria, Virtual Plants Team, 34095 Montpellier cedex 5, France.
authors.forename: Etienne
authors.initials: E
authors.lastname: Farcot
authors.affiliation: University of Missouri, Columbia, Missouri 65211.
authors.forename: Gretchen
authors.initials: G
authors.lastname: Hagen
authors.affiliation: University of Missouri, Columbia, Missouri 65211.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Guilfoyle
authors.affiliation: Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan.
authors.forename: Hidehiro
authors.initials: H
authors.lastname: Fukaki
authors.affiliation: Institut de Recherche pour le Développement, UMR DIADE, 34394 Montpellier cedex 5, France laurent.laplaze@ird.fr bennett@nottingham.ac.uk.
authors.forename: Laurent
authors.initials: L
authors.lastname: Laplaze
authors.affiliation: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough, Leicestershire LE12 5RD, United Kingdom laurent.laplaze@ird.fr bennett@nottingham.ac.uk.
authors.forename: Malcolm J
authors.initials: MJ
authors.lastname: Bennett
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics*; D002454:Cell Differentiation / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics*; D009154:Mutation; D018517:Plant Roots / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D030821:Plants, Genetically Modified; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome
chemical_list: C503425:ARF7 protein, Arabidopsis; D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; C111371:MONOPTEROS protein, Arabidopsis; D014157:Transcription Factors