ChIP-seq analysis of histone modifications at the core of the Arabidopsis circadian clock

Over the past years, chromatin modification has emerged as a key regulator of gene expression. A very useful method for chromatin analysis is chromatin immunoprecipitation (ChIP), which allows the quantification and localization of specific histone modifications. The basic steps of the ChIP protocol include cross-linking of histones and DNA, chromatin isolation, shearing the DNA into smaller fragments, immunoprecipitation with specific antibodies, and enrichment analysis by several methods including real-time quantitative PCR (ChIP-qPCR), microarray hybridization (ChIP-chip), or sequencing (ChIP-seq). Here, we describe how to use ChIP-qPCR to analyze histone modifications at the core of the Arabidopsis thaliana circadian clock. We also briefly discuss a number of protocol adjustments to be considered in ChIP-seq experiments.