title: Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure.
abstract: Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. Here we describe how ZipChIP enables detection of histone modifications (H3K4 mono- and trimethylation) and two yeast histone demethylases, Jhd2 and Rph1, which were previously difficult to detect using standard methods. Furthermore, we demonstrate the versatility of ZipChIP by analyzing the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, at euchromatin in Arabidopsis thaliana.
authors.affiliation: Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Kayla M
authors.initials: KM
authors.lastname: Harmeyer
authors.affiliation: Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Paul F
authors.initials: PF
authors.lastname: South
authors.affiliation: Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Brett
authors.initials: B
authors.lastname: Bishop
authors.affiliation: Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Joe
authors.initials: J
authors.lastname: Ogas
authors.affiliation: Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA sdbriggs@purdue.edu.
authors.forename: Scott D
authors.initials: SD
authors.lastname: Briggs
mesh_terms: D000199:Actins / Q000235:genetics / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000706:statistics & numerical data; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D005800:Genes, Fungal; D017343:Genes, Plant; D056466:Histone Demethylases / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D056565:Sirtuin 2 / Q000235:genetics / Q000378:metabolism
chemical_list: C480844:ACT7 protein, Arabidopsis; D000199:Actins; D029681:Arabidopsis Proteins; D002843:Chromatin; D004268:DNA-Binding Proteins; D006657:Histones; C400296:RPH1 protein, S cerevisiae; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae; D056466:Histone Demethylases; C519119:JHD2 protein, S cerevisiae; D056484:Jumonji Domain-Containing Histone Demethylases; C087778:SIR2 protein, S cerevisiae; D056565:Sirtuin 2; C402442:AT2G25170 protein, Arabidopsis; D004265:DNA Helicases