Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

Hamid Mirzaei, Theo A. Knijnenburg, Bong Kim, Max Robinson, Paola Picotti, Gregory W. Carter, Song Li, David J. Dilworth, Jimmy K. Eng, John D. Aitchison, Ilya Shmulevich, Timothy Galitski, Ruedi Aebersold, Jeffrey Ranish

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21 Scopus citations

Abstract

Regulation of gene expression involves the orchestrated interaction of a large number of proteins with transcriptional regulatory elements in the context of chromatin. Our understanding of gene regulation is limited by the lack of a protein measurement technology that can systematically detect and quantify the ensemble of proteins associated with the transcriptional regulatory elements of specific genes. Here, we introduce a set of selected reaction monitoring (SRM) assays for the systematic measurement of 464 proteins with known or suspected roles in transcriptional regulation at RNA polymerase II transcribed promoters in Saccharomyces cerevisiae. Measurement of these proteins in nuclear extracts by SRMpermitted the reproducible quantification of 42% of the proteins over a wide range of abundances. By deploying the assay to systematically identify DNA binding transcriptional regulators that interact with the environmentally regulated FLO11 promoter in cell extracts, we identified 15 regulators that bound specifically to distinct regions along ~600 bp of the regulatory sequence. Importantly, the dataset includes a number of regulators that have been shown to either control FLO11 expression or localize to these regulatory regions in vivo.We further validated the utility of the approach by demonstrating that two of the SRM-identified factors, Mot3 and Azf1, are required for proper FLO11 expression. These results demonstrate the utility of SRM-based targeted proteomics to guide the identification of gene-specific transcriptional regulators.

Original languageEnglish (US)
Pages (from-to)3645-3650
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume110
Issue number9
DOIs
StatePublished - Feb 26 2013

ASJC Scopus subject areas

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    Mirzaei, H., Knijnenburg, T. A., Kim, B., Robinson, M., Picotti, P., Carter, G. W., Li, S., Dilworth, D. J., Eng, J. K., Aitchison, J. D., Shmulevich, I., Galitski, T., Aebersold, R., & Ranish, J. (2013). Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proceedings of the National Academy of Sciences of the United States of America, 110(9), 3645-3650. https://doi.org/10.1073/pnas.1216918110