Identification of Brassinosteroid Target Genes by Chromatin Immunoprecipitation Followed by High-Throughput Sequencing (ChIP-seq) and RNA-Sequencing

  • Trevor Nolan
  • Sanzhen Liu
  • Hongqing Guo
  • Lei Li
  • Patrick Schnable
  • Yanhai YinEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1564)


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.

Key words

Transcription factor Target genes ChIP-seq RNA-seq Gene expression 



We thank Iowa State University DNA Facility for allowing us to use the Diagenode Bioruptor and Mike Baker for information on ChIP-seq product amplification. The work is supported by grant from NSF (IOS-1257631) and by the Plant Science Institute at Iowa State University.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Trevor Nolan
    • 1
  • Sanzhen Liu
    • 2
  • Hongqing Guo
    • 1
  • Lei Li
    • 1
    • 3
  • Patrick Schnable
    • 4
  • Yanhai Yin
    • 1
    Email author
  1. 1.Department of Genetics, Development and Cell BiologyIowa State UniversityAmesUSA
  2. 2.Department of Plant PathologyKansas State UniversityManhattanUSA
  3. 3.Harvard Medical SchoolHarvard UniversityBostonUSA
  4. 4.Department of AgronomyIowa State UniversityAmesUSA

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