HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae

Hector Guillen-Ahlers, Prahlad K. Rao, Mark E. Levenstein, Julia Kennedy-Darling, Danu S. Perumalla, Avinash Y.L. Jadhav, Jeremy P. Glenn, Amy Ludwig-Kubinski, Eugene Drigalenko, Maria J. Montoya, Harald H. Göring, Corianna D. Anderson, Mark Scalf, Heidi I.S. Gildersleeve, Regina Cole, Alexandra M. Greene, Akua K. Oduro, Katarina Lazarova, Anthony J. Cesnik, Jared BarfknechtLisa A. Cirillo, Audrey P. Gasch, Michael R. Shortreed, Lloyd M. Smith, Michael Olivier

    Research output: Contribution to journalArticlepeer-review

    8 Scopus citations

    Abstract

    Currently available methods for interrogating DNA-protein interactions at individual genomic loci have significant limitations, and make it difficult to work with unmodified cells or examine single-copy regions without specific antibodies. In this study, we describe a physiological application of the Hybridization Capture of Chromatin-Associated Proteins for Proteomics (HyCCAPP) methodology we have developed. Both novel and known locus-specific DNA-protein interactions were identified at the ENO2 and GAL1 promoter regions of Saccharomyces cerevisiae, and revealed subgroups of proteins present in significantly different levels at the loci in cells grown on glucose versus galactose as the carbon source. Results were validated using chromatin immunoprecipitation. Overall, our analysis demonstrates that HyCCAPP is an effective and flexible technology that does not require specific antibodies nor prior knowledge of locally occurring DNA-protein interactions and can now be used to identify changes in protein interactions at target regions in the genome in response to physiological challenges.

    Original languageEnglish (US)
    Pages (from-to)267-273
    Number of pages7
    JournalGenomics
    Volume107
    Issue number6
    DOIs
    StatePublished - 2016

    Keywords

    • Chromatin
    • Chromatin immunoprecipitation
    • DNA-protein interactions
    • ENO2
    • Proteomics
    • Yeast

    ASJC Scopus subject areas

    • Genetics

    Fingerprint Dive into the research topics of 'HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae'. Together they form a unique fingerprint.

    Cite this