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R-DeeP: proteome-wide and quantitative identification of RNA-dependent proteins by density gradient ultracentrifugation

Summary - The comprehensive but specific identification of RNA-binding proteins as well as the discovery of RNA-associated protein functions remain major challenges in RNA biology. Here we adapt the concept of RNA dependence, defining a protein as RNA dependent when its interactome depends on RNA. W...

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Hauptverfasser: Caudron-Herger, Maïwen (Verfasst von) , Rusin, Scott F. (Verfasst von) , Adamo, Mark E. (Verfasst von) , Seiler, Jeanette (Verfasst von) , Schmid, Vera K. (Verfasst von) , Barreau, Elsa (Verfasst von) , Kettenbach, Arminja Nadine (Verfasst von) , Diederichs, Sven (Verfasst von)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: May 7, 2019
In: Molecular cell
Year: 2019, Jahrgang: 75, Heft: 1, Pages: 184-199.e10
ISSN:1097-4164
DOI:10.1016/j.molcel.2019.04.018
Online-Zugang:Verlag, Volltext: https://doi.org/10.1016/j.molcel.2019.04.018
Verlag, Volltext: http://www.sciencedirect.com/science/article/pii/S1097276519303107
Volltext
Verfasserangaben:Maiwen Caudron-Herger, Scott F. Rusin, Mark E. Adamo, Jeanette Seiler, Vera K. Schmid, Elsa Barreau, Arminja N. Kettenbach, Sven Diederichs
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Zusammenfassung:Summary - The comprehensive but specific identification of RNA-binding proteins as well as the discovery of RNA-associated protein functions remain major challenges in RNA biology. Here we adapt the concept of RNA dependence, defining a protein as RNA dependent when its interactome depends on RNA. We converted this concept into a proteome-wide, unbiased, and enrichment-free screen called R-DeeP (RNA-dependent proteins), based on density gradient ultracentrifugation. Quantitative mass spectrometry identified 1,784 RNA-dependent proteins, including 537 lacking known links to RNA. Exploiting the quantitative nature of R-DeeP, proteins were classified as not, partially, or completely RNA dependent. R-DeeP identified the transcription factor CTCF as completely RNA dependent, and we uncovered that RNA is required for the CTCF-chromatin association. Additionally, R-DeeP allows reconstruction of protein complexes based on co-segregation. The whole dataset is available at http://R-DeeP.dkfz.de, providing proteome-wide, specific, and quantitative identification of proteins with RNA-dependent interactions and aiming at future functional discovery of RNA-protein complexes.
Beschreibung:Gesehen am 29.08.2019
Beschreibung:Online Resource
ISSN:1097-4164
DOI:10.1016/j.molcel.2019.04.018

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