title: Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.
abstract: Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors.
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Erin E
authors.initials: EE
authors.lastname: Sparks
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Colleen
authors.initials: C
authors.lastname: Drapek
authors.affiliation: Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA.
authors.forename: Allison
authors.initials: A
authors.lastname: Gaudinier
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: Mitra
authors.initials: M
authors.lastname: Ansariola
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Shen
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Jessica H
authors.initials: JH
authors.lastname: Hennacy
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Jingyuan
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA.
authors.forename: Gina
authors.initials: G
authors.lastname: Turco
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Jalean J
authors.initials: JJ
authors.lastname: Petricka
authors.affiliation: Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Foret
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Computer Science, Duke University, Durham, NC 27708, USA.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Hartemink
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA.
authors.forename: Raluca
authors.initials: R
authors.lastname: Gordân
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Megraw
authors.affiliation: Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA.
authors.forename: Siobhan M
authors.initials: SM
authors.lastname: Brady
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA. Electronic address: philip.benfey@duke.edu.
authors.forename: Philip N
authors.initials: PN
authors.lastname: Benfey
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D003198:Computer Simulation; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D017930:Genes, Reporter; D005813:Genes, Synthetic; D008957:Models, Genetic; D018517:Plant Roots / Q000166:cytology / Q000378:metabolism; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*; D020798:Two-Hybrid System Techniques
chemical_list: D029681:Arabidopsis Proteins; D012097:Repressor Proteins; C100978:SCR protein, Arabidopsis; C410510:SHORT ROOT protein, Arabidopsis; D015534:Trans-Activators; D014157:Transcription Factors
keywords: Arabidopsis; SCARECROW; SHORTROOT; roots; transcription factor