title: A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana.
abstract: Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. The transcriptional network through which BES1 and BZR regulate large number of target genes is mostly unknown. By combining chromatin immunoprecipitation coupled with Arabidopsis tiling arrays (ChIP-chip) and gene expression studies, we have identified 1609 putative BES1 target genes, 404 of which are regulated by BRs and/or in gain-of-function bes1-D mutant. BES1 targets contribute to BR responses and interactions with other hormonal or light signaling pathways. Computational modeling of gene expression data using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) reveals that BES1-targeted transcriptional factors form a gene regulatory network (GRN). Mutants of many genes in the network displayed defects in BR responses. Moreover, we found that BES1 functions to inhibit chloroplast development by repressing the expression of GLK1 and GLK2 transcription factors, confirming a hypothesis generated from the GRN. Our results thus provide a global view of BR regulated gene expression and a GRN that guides future studies in understanding BR-regulated plant growth.
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Yu
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Jaroslaw
authors.initials: J
authors.lastname: Zola
authors.forename: Maneesha
authors.initials: M
authors.lastname: Aluru
authors.forename: Huaxun
authors.initials: H
authors.lastname: Ye
authors.forename: Andrew
authors.initials: A
authors.lastname: Foudree
authors.forename: Hongqing
authors.initials: H
authors.lastname: Guo
authors.forename: Sarah
authors.initials: S
authors.lastname: Anderson
authors.forename: Srinivas
authors.initials: S
authors.lastname: Aluru
authors.forename: Peng
authors.initials: P
authors.lastname: Liu
authors.forename: Steve
authors.initials: S
authors.lastname: Rodermel
authors.forename: Yanhai
authors.initials: Y
authors.lastname: Yin
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D004268:DNA-Binding Proteins; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D010937:Plant Growth Regulators / Q000378:metabolism*; D013256:Steroids / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; C456160:BES1 protein, Arabidopsis; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D010937:Plant Growth Regulators; D013256:Steroids; D014157:Transcription Factors