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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.
- 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.)
- Subjects :
- Centrifugation, Density Gradient instrumentation
Chromatin chemistry
Chromatin metabolism
Gene Expression Regulation
Gene Ontology
HeLa Cells
Humans
Information Dissemination
Internet
Molecular Sequence Annotation
Protein Binding
Proteome classification
Proteome metabolism
Proteomics methods
RNA metabolism
RNA-Binding Proteins classification
RNA-Binding Proteins metabolism
Transcription Factors classification
Transcription Factors metabolism
Centrifugation, Density Gradient methods
Protein Interaction Maps
Proteome genetics
RNA genetics
RNA-Binding Proteins genetics
Transcription Factors genetics
Subjects
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