title: Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-Throughput Sequencing (ChIP-seq) and RNA-Sequencing.
abstract: Brassinosteroids (BRs) play important roles in many growth and developmental processes. BRs signal to regulate BR-INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1 (BES1) and BRASSINAZOLE-RESISTANT1 (BZR1) transcription factors (TFs), which, in turn, regulate several hundreds of transcription factors (termed BES1/BZR1-targeted TFs or BTFs) and thousands of genes to mediate various BR responses. Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-seq) with BES1/BZR1 and BTFs is an important approach to identify BR target genes. In combination with RNA-sequencing experiments, these genomic methods have become powerful tools to detect BR target genes and reveal transcriptional networks underlying BR-regulated processes.
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011-3650, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Nolan
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.
authors.forename: Sanzhen
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011-3650, USA.
authors.forename: Hongqing
authors.initials: H
authors.lastname: Guo
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011-3650, USA.|Harvard Medical School, Harvard University, Boston, MA, 02114-2790, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA, 50011-3650, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schnable
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011-3650, USA. yin@iastate.edu.
authors.forename: Yanhai
authors.initials: Y
authors.lastname: Yin
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D060406:Brassinosteroids / Q000494:pharmacology*; D047369:Chromatin Immunoprecipitation / Q000379:methods; D019295:Computational Biology; D004268:DNA-Binding Proteins; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D010937:Plant Growth Regulators / Q000494:pharmacology*; D036226:Seedlings / Q000187:drug effects / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D015398:Signal Transduction; D013260:Steroids, Heterocyclic / Q000494:pharmacology*
chemical_list: D029681:Arabidopsis Proteins; C456160:BES1 protein, Arabidopsis; C454444:BZR1 protein, Arabidopsis; D060406:Brassinosteroids; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D010937:Plant Growth Regulators; D013260:Steroids, Heterocyclic; C023623:brassinolide
keywords: ChIP-seq; Gene expression; RNA-seq; Target genes; Transcription factor