title: Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.
abstract: DNA-protein interactions play critical roles in the control of genome expression and other fundamental processes. An essential element in understanding how these systems function is to identify their molecular components. We present here a novel strategy, Hybridization Capture of Chromatin Associated Proteins for Proteomics (HyCCAPP), to identify proteins that are interacting with any given region of the genome. This technology identifies and quantifies the proteins that are specifically interacting with a genomic region of interest by sequence-specific hybridization capture of the target region from in vivo cross-linked chromatin, followed by mass spectrometric identification and quantification of associated proteins. We demonstrate the utility of HyCCAPP by identifying proteins associated with three multicopy and one single-copy loci in yeast. In each case, a locus-specific pattern of target-associated proteins was revealed. The binding of previously unknown proteins was confirmed by ChIP in 11 of 17 cases. The identification of many previously known proteins at each locus provides strong support for the ability of HyCCAPP to correctly identify DNA-associated proteins in a sequence-specific manner, while the discovery of previously unknown proteins provides new biological insights into transcriptional and regulatory processes at the target locus.
authors.forename: Julia
authors.initials: J
authors.lastname: Kennedy-Darling
authors.affiliation: ‡Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States.
authors.forename: Hector
authors.initials: H
authors.lastname: Guillen-Ahlers
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shortreed
authors.forename: Mark
authors.initials: M
authors.lastname: Scalf
authors.forename: Brian L
authors.initials: BL
authors.lastname: Frey
authors.forename: Christina
authors.initials: C
authors.lastname: Kendziorski
authors.affiliation: ‡Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Olivier
authors.forename: Audrey P
authors.initials: AP
authors.lastname: Gasch
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D002843:Chromatin / Q000737:chemistry*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000378:metabolism; D013058:Mass Spectrometry; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D025941:Protein Interaction Mapping; D020543:Proteome / Q000378:metabolism; D040901:Proteomics; D012270:Ribosomes / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA
keywords: ChIP; DNA-binding proteins; DNA−protein interactions; GENECAPP; HyCCAPP; X-element; chromatin; chromatin immunoprecipitation; hybridization; mass spectrometry; proteomics; rDNA; ribosome biogenesis; transcription factors; transcriptional regulation