title: Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
abstract: The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of eukaryotic genomes. We developed a digital approach to assay regulatory protein occupancy on genomic DNA in vivo by dense mapping of individual DNase I cleavages from intact nuclei using massively parallel DNA sequencing. Analysis of >23 million cleavages across the Saccharomyces cerevisiae genome revealed thousands of protected regulatory protein footprints, enabling de novo derivation of factor binding motifs and the identification of hundreds of new binding sites for major regulators. We observed striking correspondence between single-nucleotide resolution DNase I cleavage patterns and protein-DNA interactions determined by crystallography. The data also yielded a detailed view of larger chromatin features including positioned nucleosomes flanking factor binding regions. Digital genomic footprinting should be a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, USA.
authors.forename: Jay R
authors.initials: JR
authors.lastname: Hesselberth
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Chen
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Zhang
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Sabo
authors.forename: Richard
authors.initials: R
authors.lastname: Sandstrom
authors.forename: Alex P
authors.initials: AP
authors.lastname: Reynolds
authors.forename: Robert E
authors.initials: RE
authors.lastname: Thurman
authors.forename: Shane
authors.initials: S
authors.lastname: Neph
authors.forename: Michael S
authors.initials: MS
authors.lastname: Kuehn
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.forename: Stanley
authors.initials: S
authors.lastname: Fields
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D018983:DNA Footprinting / Q000379:methods*; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics*
chemical_list: D014157:Transcription Factors; D004247:DNA