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 Yin

doi:10.1007/978-1-4939-6813-8_7

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

Methods Mol Biol. 2017:1564:63-79. doi: 10.1007/978-1-4939-6813-8_7.

Authors

Trevor Nolan¹, Sanzhen Liu², Hongqing Guo¹, Lei Li^{1

3}, Patrick Schnable⁴, Yanhai Yin⁵

Affiliations

¹ Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011-3650, USA.
² Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA.
³ Harvard Medical School, Harvard University, Boston, MA, 02114-2790, USA.
⁴ Department of Agronomy, Iowa State University, Ames, IA, 50011-3650, USA.
⁵ Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011-3650, USA. yin@iastate.edu.

PMID: 28124247
DOI: 10.1007/978-1-4939-6813-8_7

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.

Keywords: ChIP-seq; Gene expression; RNA-seq; Target genes; Transcription factor.

MeSH terms

Arabidopsis / drug effects
Arabidopsis / genetics*
Arabidopsis / growth & development
Arabidopsis / metabolism
Arabidopsis Proteins / genetics*
Arabidopsis Proteins / metabolism
Brassinosteroids / pharmacology*
Chromatin Immunoprecipitation / methods
Computational Biology
DNA-Binding Proteins
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant*
High-Throughput Nucleotide Sequencing / methods
Nuclear Proteins / genetics*
Nuclear Proteins / metabolism
Plant Growth Regulators / pharmacology*
Seedlings / drug effects
Seedlings / genetics
Seedlings / growth & development
Seedlings / metabolism
Signal Transduction
Steroids, Heterocyclic / pharmacology*

Substances

Arabidopsis Proteins
BES1 protein, Arabidopsis
BZR1 protein, Arabidopsis
Brassinosteroids
DNA-Binding Proteins
Nuclear Proteins
Plant Growth Regulators
Steroids, Heterocyclic
brassinolide