Nearly all signal transduction pathways lead to regulation of gene
expression by controlling specific transcription factors (TFs).
Chromatin immunoprecipitation (ChIP) is a powerful method for studying
TF–DNA interactions in vivo. To identify all binding sites of a TF in the
genome, the DNA obtained in ChIP experiments needs to be analyzed by
hybridization to genome-tiling microarrays (ChIP-chip) or by
next-generation sequencing (ChIP-seq). Here, we provide detailed
protocols of ChIP for two model plant species Arabidopsis and rice,
procedures of DNA sample preparation for ChIP-chip or ChIP-seq, and a
general guide for computational data analysis. We have used these
protocols to successfully identify direct target genes of the BZR1 TF of
the brassinosteroid signaling pathway in both Arabidopsis and rice.
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