title: Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.
abstract: Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. We mapped DNase I hypersensitive sites (DHSs) in A. thaliana seedlings and used genomic footprinting to delineate ∼ 700,000 sites of in vivo transcription factor (TF) occupancy at nucleotide resolution. We show that variation associated with 72 diverse quantitative phenotypes localizes within DHSs. TF footprints encode an extensive cis-regulatory lexicon subject to recent evolutionary pressures, and widespread TF binding within exons may have shaped codon usage patterns. The architecture of A. thaliana TF regulatory networks is strikingly similar to that of animals in spite of diverged regulatory repertoires. We analyzed regulatory landscape dynamics during heat shock and photomorphogenesis, disclosing thousands of environmentally sensitive elements and enabling mapping of key TF regulatory circuits underlying these fundamental responses. Our results provide an extensive resource for the study of A. thaliana gene regulation and functional biology.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Alessandra M
authors.initials: AM
authors.lastname: Sullivan
authors.affiliation: Department of Biology, University of Washington, Seattle, WA 98195, USA.
authors.forename: Andrej A
authors.initials: AA
authors.lastname: Arsovski
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Janne
authors.initials: J
authors.lastname: Lempe
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Kerry L
authors.initials: KL
authors.lastname: Bubb
authors.affiliation: Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Weirauch
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Sabo
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Sandstrom
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Thurman
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Shane
authors.initials: S
authors.lastname: Neph
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Alex P
authors.initials: AP
authors.lastname: Reynolds
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Andrew B
authors.initials: AB
authors.lastname: Stergachis
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Vernot
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Audra K
authors.initials: AK
authors.lastname: Johnson
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Haugen
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Shawn T
authors.initials: ST
authors.lastname: Sullivan
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Thompson
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Fidencio V
authors.initials: FV
authors.lastname: Neri
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Weaver
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Morgan
authors.initials: M
authors.lastname: Diegel
authors.affiliation: Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada.
authors.forename: Sanie
authors.initials: S
authors.lastname: Mnaimneh
authors.affiliation: Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada.
authors.forename: Ally
authors.initials: A
authors.lastname: Yang
authors.affiliation: Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto ON M5S 3E1, Canada; Canadian Institute for Advanced Research (CIFAR) Program in Genetic Networks, Toronto ON M5G 1Z8, Canada.
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
authors.affiliation: Department of Biology, University of Washington, Seattle, WA 98195, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Nemhauser
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address: queitsch@uw.edu.
authors.forename: Christine
authors.initials: C
authors.lastname: Queitsch
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address: jstam@uw.edu.
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D002874:Chromosome Mapping; D003062:Codon; D003850:Deoxyribonuclease I / Q000378:metabolism; D005091:Exons; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D008027:Light; D063245:Plant Development / Q000235:genetics; D011485:Protein Binding; D050436:Regulatory Elements, Transcriptional / Q000235:genetics; D036226:Seedlings / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D003062:Codon; D014157:Transcription Factors; D003850:Deoxyribonuclease I