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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| Main Authors: | , , , , , , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
May 7, 2019
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| In: |
Molecular cell
Year: 2019, Volume: 75, Issue: 1, Pages: 184-199.e10 |
| ISSN: | 1097-4164 |
| DOI: | 10.1016/j.molcel.2019.04.018 |
| Online Access: | Verlag, Volltext: https://doi.org/10.1016/j.molcel.2019.04.018 Verlag, Volltext: http://www.sciencedirect.com/science/article/pii/S1097276519303107 
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| Author Notes: | Maiwen Caudron-Herger, Scott F. Rusin, Mark E. Adamo, Jeanette Seiler, Vera K. Schmid, Elsa Barreau, Arminja N. Kettenbach, Sven Diederichs |
| Summary: | 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. |
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| Item Description: | Gesehen am 29.08.2019 |
| Physical Description: | Online Resource |
| ISSN: | 1097-4164 |
| DOI: | 10.1016/j.molcel.2019.04.018 |