Chromatin immunoprecipitation to characterize the epigenetic profiles of imprinted domains.
Imprinted genes are marked by parental allele specific DNA methylation and histone modifications which regulate their monoallelic expression. Chromatin immunoprecipitation (ChIP) is the technique of choice to characterize the histones associated with either maternal or paternal chromosomes. To study allele-specific chromatin composition at imprinted regions, the method has to be efficient to work on limiting amount of starting material, and specific enough to recognize one of the parental alleles. We optimized the commonly used ChIP technique for efficient recovery of one parental allele from small number of cells. We provide examples to show that this ChIP protocol can specifically distinguish between parental alleles in mouse embryo fibroblasts carrying maternal and paternal duplication of mouse distal Chr7 and also in normal mouse embryo fibroblasts carrying single nucleotide polymorphism at imprinted regions.
Department of Molecular and Cellular Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, USA. psingh@coh.org
Purnima
P
Singh
Piroska E
PE
Szabó
D000483:Alleles; D000818:Animals; D002469:Cell Separation; D002843:Chromatin / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D019286:Endopeptidase K / Q000378:metabolism; D044127:Epigenesis, Genetic; D018392:Genomic Imprinting / Q000235:genetics*; D006657:Histones / Q000235:genetics; D051379:Mice; D060888:Real-Time Polymerase Chain Reaction; D013010:Sonication
D002843:Chromatin; D006657:Histones; D004247:DNA; D019286:Endopeptidase K