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R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation.

R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation.

Authors :
Caudron-Herger M
Rusin SF
Adamo ME
Seiler J
Schmid VK
Barreau E
Kettenbach AN
Diederichs S
Source :
Molecular cell [Mol Cell] 2019 Jul 11; Vol. 75 (1), pp. 184-199.e10. Date of Electronic Publication: 2019 May 07.
Publication Year :
2019

Abstract

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.<br /> (Copyright © 2019 Elsevier Inc. All rights reserved.)

Details

Language :
English
ISSN :
1097-4164
Volume :
75
Issue :
1
Database :
MEDLINE
Journal :
Molecular cell
Publication Type :
Academic Journal
Accession number :
31076284
Full Text :
https://doi.org/10.1016/j.molcel.2019.04.018