title: Genomic footprinting.
abstract: The advent of DNA footprinting with DNase I more than 35 years ago enabled the systematic analysis of protein-DNA interactions, and the technique has been instrumental in the decoding of cis-regulatory elements and the identification and characterization of transcription factors and other DNA-binding proteins. The ability to analyze millions of individual genomic cleavage events via massively parallel sequencing has enabled in vivo DNase I footprinting on a genomic scale, offering the potential for global analysis of transcription factor occupancy in a single experiment. Genomic footprinting has opened unique vistas on the organization, function and evolution of regulatory DNA; however, the technology is still nascent. Here we discuss both prospects and challenges of genomic footprinting, as well as considerations for its application to complex genomes.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.|Altius Institute for Biomedical Sciences, Seattle, Washington, USA.
authors.forename: Jeff
authors.identifier: http://orcid.org/0000-0001-6406-8563
authors.initials: J
authors.lastname: Vierstra
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.|Altius Institute for Biomedical Sciences, Seattle, Washington, USA.|Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000235:genetics*; D018983:DNA Footprinting / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans
chemical_list: D004247:DNA