Chromatin Immunoprecipitation in Crops

Chromatin immunoprecipitation (ChIP) is a well-established technique that allows for the identification of genomic regions where proteins such as transcription factors, histones, or other chromatin-associated proteins bind. Moreover, deep sequencing of immunoprecipitated DNA (ChIP-seq) provides unbiased genome-wide insights into these binding sites. This chapter describes a detailed ChIP protocol tailored for transcription factors in recalcitrant plant leaves, using the commercial strawberry, the octoploid species Fragaria × ananassa, as an example. This protocol ensures obtaining DNA of both high quality and quantity for subsequent library preparation for Illumina sequencing. Finally, this chapter also details how to conduct quantitative PCR to validate the enrichment of the TF binding sites.