TY - JOUR
T1 - HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae
AU - Guillen-Ahlers, Hector
AU - Rao, Prahlad K.
AU - Levenstein, Mark E.
AU - Kennedy-Darling, Julia
AU - Perumalla, Danu S.
AU - Jadhav, Avinash Y.L.
AU - Glenn, Jeremy P.
AU - Ludwig-Kubinski, Amy
AU - Drigalenko, Eugene
AU - Montoya, Maria J.
AU - Göring, Harald H.
AU - Anderson, Corianna D.
AU - Scalf, Mark
AU - Gildersleeve, Heidi I.S.
AU - Cole, Regina
AU - Greene, Alexandra M.
AU - Oduro, Akua K.
AU - Lazarova, Katarina
AU - Cesnik, Anthony J.
AU - Barfknecht, Jared
AU - Cirillo, Lisa A.
AU - Gasch, Audrey P.
AU - Shortreed, Michael R.
AU - Smith, Lloyd M.
AU - Olivier, Michael
N1 - Funding Information:
This work was supported in part by NIH/NHGRI grant P50HG004952 and NIH/NIGMS grant R01 GM109099. A.J.C. was supported by the Computation and Informatics in Biology and Medicine Training Program 5T15LM007359.
Publisher Copyright:
© 2016 Elsevier Inc.
PY - 2016
Y1 - 2016
N2 - 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.
AB - 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.
KW - Chromatin
KW - Chromatin immunoprecipitation
KW - DNA-protein interactions
KW - ENO2
KW - Proteomics
KW - Yeast
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U2 - 10.1016/j.ygeno.2016.05.002
DO - 10.1016/j.ygeno.2016.05.002
M3 - Article
C2 - 27184763
AN - SCOPUS:84969263291
SN - 0888-7543
VL - 107
SP - 267
EP - 273
JO - Genomics
JF - Genomics
IS - 6
ER -