title: Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties.
abstract: OsMADS1 controls rice (Oryza sativa) floral fate and organ development. Yet, its genome-wide targets and the mechanisms underlying its role as a transcription regulator controlling developmental gene expression are unknown. We identify 3112 gene-associated OsMADS1-bound sites in the floret genome. These occur in the vicinity of transcription start sites, within gene bodies, and in intergenic regions. Majority of the bound DNA contained CArG motif variants or, in several cases, only A-tracts. Sequences flanking the binding peak had a higher AT nucleotide content, implying that broader DNA structural features may define in planta binding. Sequences for binding by other transcription factor families like MYC, AP2/ERF, bZIP, etc. are enriched in OsMADS1-bound DNAs. Target genes implicated in transcription, chromatin remodeling, cellular processes, and hormone metabolism were enriched. Combining expression data from OsMADS1 knockdown florets with these DNA binding data, a snapshot of a gene regulatory network was deduced where targets, such as AP2/ERF and bHLH transcription factors and chromatin remodelers form nodes. We show that the expression status of these nodal factors can be altered by inducing the OsMADS1-GR fusion protein and present a model for a regulatory cascade where the direct targets of OsMADS1, OsbHLH108/SPT, OsERF034, and OsHSF24, in turn control genes such as OsMADS32 and OsYABBY5 This cascade, with other similar relationships, cumulatively contributes to floral organ development. Overall, OsMADS1 binds to several regulatory genes and, probably in combination with other factors, controls a gene regulatory network that ensures rice floret development.
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.).
authors.forename: Imtiyaz
authors.initials: I
authors.lastname: Khanday
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.).
authors.forename: Sanjukta
authors.initials: S
authors.lastname: Das
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.).
authors.forename: Grace L
authors.initials: GL
authors.lastname: Chongloi
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.).
authors.forename: Manju
authors.identifier: 0000-0003-4218-0559
authors.initials: M
authors.lastname: Bansal
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.).
authors.forename: Ueli
authors.identifier: 0000-0002-0522-8974
authors.initials: U
authors.lastname: Grossniklaus
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.) uvr@mcbl.iisc.ernet.in.
authors.forename: Usha
authors.initials: U
authors.lastname: Vijayraghavan
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant / Q000235:genetics*; D026161:MADS Domain Proteins / Q000235:genetics* / Q000378:metabolism; D059372:Nucleotide Motifs / Q000235:genetics; D012275:Oryza / Q000235:genetics / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D030821:Plants, Genetically Modified; D011485:Protein Binding; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D026161:MADS Domain Proteins; D010940:Plant Proteins; D014157:Transcription Factors