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HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics 2016 06;107(6):267-73

Date

05/18/2016

Pubmed ID

27184763

Pubmed Central ID

PMC5017017

DOI

10.1016/j.ygeno.2016.05.002

Scopus ID

2-s2.0-84969263291   8 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.

Author List

Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AY, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HI, Cole R, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M

Author

Lisa A. Cirillo PhD Assistant Dean, Associate Professor in the Cell Biology, Neurobiology and Anatomy department at Medical College of Wisconsin




MESH terms used to index this publication - Major topics in bold

Chromatin
Chromatin Immunoprecipitation
DNA-Binding Proteins
Galactokinase
Phosphopyruvate Hydratase
Promoter Regions, Genetic
Protein Binding
Proteomics
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins