title: Genome-wide localization of replication factors.
abstract: Chromatin Immunoprecipitation (ChIP) is a powerful tool for the identification and characterization of protein-DNA interactions in vivo. ChIP has been utilized to study diverse nuclear processes such as transcription regulation, chromatin modification, DNA recombination and DNA replication at specific loci and, more recently, across the entire genome. Advances in genomic approaches, and whole genome sequencing in particular, have made it possible and affordable to comprehensively identify specific protein binding sites throughout the genomes of higher eukaryotes. The dynamic nature of the DNA replication program and the transient occupancy of many replication factors throughout the cell cycle present additional challenges that may not pertain to the mapping of site specific transcription factors. Here we discuss the specific considerations that need to be addressed in the application of ChIP to the genome-wide location analysis of protein factors involved in DNA replication.
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
authors.forename: Yoav
authors.initials: Y
authors.lastname: Lubelsky
authors.forename: Heather K
authors.initials: HK
authors.lastname: MacAlpine
authors.forename: David M
authors.initials: DM
authors.lastname: MacAlpine
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D053837:DNA Cleavage; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000302:isolation & purification* / Q000378:metabolism; D004330:Drosophila / Q000166:cytology / Q000235:genetics; D029721:Drosophila Proteins / Q000302:isolation & purification* / Q000378:metabolism; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011485:Protein Binding; D018741:Replication Origin; D016707:Tissue Fixation
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D005404:Fixatives; D005557:Formaldehyde; D004247:DNA