title: DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution by Pyrosequencing®.
abstract: Interaction and co-occurrence of protein and DNA-based epigenetic modifications 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 specifically associated with a protein of interest. First, DNA that directly interacts with the selected protein (such as a specific histone modification, a transcription factor, or any other DNA-associated protein) is purified by standard chromatin immunoprecipitation (ChIP). Second, the level of DNA methylation of this immunoprecipitated DNA is measured by bisulfite conversion and Pyrosequencing, a quantitative sequencing-by-synthesis method. This procedure allows determining the methylation status of genomic DNA associated to a specific protein at single nucleotide resolution.
authors.affiliation: Unité de Service et de Recherche CNRS-Pierre Fabre n°3388, Epigenetic Targeting of Cancer (ETaC), Toulouse, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Moison
authors.forename: Fanny
authors.initials: F
authors.lastname: Assemat
authors.forename: Antoine
authors.initials: A
authors.lastname: Daunay
authors.forename: Paola B
authors.initials: PB
authors.lastname: Arimondo
authors.forename: Jörg
authors.initials: J
authors.lastname: Tost
mesh_terms: D053000:Analytic Sample Preparation Methods; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D019175:DNA Methylation / Q000187:drug effects; D017931:DNA Primers / Q000235:genetics; D006801:Humans; D008863:Microspheres; D009711:Nucleotides / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000494:pharmacology
chemical_list: D017931:DNA Primers; D009711:Nucleotides; D013447:Sulfites; D004247:DNA; C042345:hydrogen sulfite