Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography.
Chromatin immunoprecipitation (ChIP) is routinely used to examine epigenetic modification of histones at specific genomic locations. However, covalent modifications of histone tails can serve as docking sites for chromatin regulatory factors. As such, association of these regulatory factors with chromatin could cause steric hindrance for antibody recognition, resulting in an underestimation of the relative enrichment of a given histone modification at specific loci. To overcome this problem, we have developed a native ChIP protocol to study covalent modification of histones that takes advantage of hydroxyapatite (HAP) chromatography to wash away chromatin-associated proteins before the immunoprecipitation of nucleosomes. This fast and simple procedure consists of five steps: nuclei isolation from cultured cells; fragmentation of chromatin using MNase; purification of nucleosomes using HAP; immunoprecipitation of modified nucleosomes; and qPCR analysis of DNA associated with modified histones. Nucleosomes prepared in this manner are free of contaminating proteins and permit an accurate evaluation of relative abundance of different covalent histone modifications at specific genomic loci. Completion of this protocol requires approximately 1.5 d.
Brand
Marjorie
M
Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Health Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, Ontario K1H 8L6, Canada. mbrand@ohri.ca
Rampalli
Shravanti
S
Chaturvedi
Chandra-Prakash
CP
Dilworth
F Jeffrey
FJ
D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002845:Chromatography / Q000379:methods*; D017886:Durapatite / Q000737:chemistry; D044127:Epigenesis, Genetic / Q000235:genetics; D000939:Epitopes / Q000032:analysis; D009707:Nucleosomes / Q000235:genetics / Q000276:immunology*; D016133:Polymerase Chain Reaction / Q000379:methods
D000939:Epitopes; D009707:Nucleosomes; D017886:Durapatite