DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution by Pyrosequencing®

International audienceInteraction and co-occurrence of protein and DNA-based epigenetic modifi cations have become a topic of interest for many fundamental and biomedical questions. We describe within this chapter a protocol that combines two techniques in order to determine the methylation status of the DNA specifi cally associated with a protein of interest. First, DNA that directly interacts with the selected protein (such as a specifi c histone modifi cation, a transcription factor, or any other DNA-associated protein) is purifi ed by standard chromatin immunoprecipitation (ChIP). Second, the level of DNA methylation of this immunoprecipitated DNA is measured by bisulfi te conversion and Pyrosequencing, a quantitative sequencing-by-synthesis method. This procedure allows determining the methylation status of genomic DNA associated to a specifi c protein at single nucleotide resolution