title: ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions.
abstract: Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP-seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches - for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins - provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.
authors.affiliation: Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, CB#7264, Chapel Hill, North Carolina 27599, USA. tsfurey@email.unc.edu
authors.forename: Terrence S
authors.initials: TS
authors.lastname: Furey
mesh_terms: D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000592:standards / Q000639:trends; D004247:DNA / Q000235:genetics / Q000378:metabolism; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods; D016324:Sequence Tagged Sites
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D006657:Histones; D004247:DNA