Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage1,6,
- Tessy Korthout1,6,
- Christine E. Cucinotta2,
- Ila van Kruijsbergen1,
- Tibor van Welsem1,
- Dris El Atmioui3,4,
- Huib Ovaa3,4,
- Toshio Tsukiyama2 and
- Fred van Leeuwen1,5
- 1Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands;
- 2Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
- 3Leiden Institute for Chemical Immunology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands;
- 4Oncode Institute, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- 5Department of Medical Biology, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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↵6 These authors contributed equally to this work.
Abstract
Transcription of a chromatin template involves the concerted interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here we used Epi-Decoder in yeast to systematically decode, at one transcribed locus, the chromatin binding changes of hundreds of proteins in parallel upon perturbation of transcription. By taking advantage of improved Epi-Decoder libraries, we observed broad rewiring of local chromatin proteomes following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals, eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell–specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding dynamics of multiple chromatin proteins under varying conditions and cell states. The systematic and comprehensive delineation of dynamic local chromatin proteomes will greatly aid in uncovering protein–protein relationships and protein functions at the chromatin template.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.256255.119.
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Freely available online through the Genome Research Open Access option.
- Received August 30, 2019.
- Accepted March 11, 2020.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
