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.
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The work in our laboratory is supported by grants from the Ramón Areces Foundation, the Spanish Ministry of Science and Innovation (MICINN) (BIO2010-16483), the EMBO YIP program and from EUROHORCS (European Heads of Research Councils) and the European Science Foundation (ESF) through the EURYI Award to Paloma Mas. We thank Rossana Henriques for critical comments on the manuscript.
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