title: A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana.
abstract: Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve the DNA-binding preferences of individual members. Here, we present a TF-target gene identification workflow based on the integration of novel protein binding microarray data with gene expression and multi-species promoter sequence conservation to identify the DNA-binding specificities and the gene regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application of complementary functional genomics filters, makes it possible to translate, for each TF, protein binding microarray data into a set of high-quality target genes. With this approach, we confirm NAC target genes reported from independent in vivo analyses. We emphasize that candidate target gene sets together with the workflow associated with functional modules offer a strong resource to unravel the regulatory potential of NAC genes and that this workflow could be used to study other families of transcription factors.
authors.affiliation: Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Lindemose
authors.affiliation: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Jensen
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Van de Velde
authors.affiliation: Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
authors.forename: Charlotte
authors.initials: C
authors.lastname: O'Shea
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Ken S
authors.initials: KS
authors.lastname: Heyndrickx
authors.affiliation: Center for Biological Sequence Analysis, Institute for Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Workman
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
authors.affiliation: Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark KSkriver@bio.ku.dk.
authors.forename: Karen
authors.initials: K
authors.lastname: Skriver
authors.affiliation: Center for Biological Sequence Analysis, Institute for Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark fdemasi@cbs.dtu.dk.
authors.forename: Federico
authors.initials: F
authors.lastname: De Masi
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D001665:Binding Sites; D018744:DNA, Plant / Q000737:chemistry / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; C508066:At3g15510 protein, Arabidopsis; D012097:Repressor Proteins; D014157:Transcription Factors