R-DeeP-related Publications

List of R-DeeP-based publications and similar concepts

Below, you will find a list of proteome-wide screens based on our R-DeeP methodology (Caudron-Herger et al., Mol Cell, 2019, first on the list) and similar concepts to identify RNA-dependent proteins by us and others.

 

  1. Caudron-Herger, M. et al. R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. Mol Cell 75, 184-199.e10 (2019). https://doi.org/10.1016/j.molcel.2019.04.018

  2. Mallam, A. L. et al. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Reports29, 1351-1368.e5 (2019). https://doi.org/10.1016/j.celrep.2019.09.060

  3. Caudron-Herger, M. et al. Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. Nat Protoc 15, 1338–1370 (2020). https://doi.org/10.1038/s41596-019-0261-4

  4. Gerovac, M. et al. Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. RNA 26, rna.076992.120 (2020). https://doi.org/10.1261/rna.076992.120

  5. Rajagopal, V. et al. Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells. Cancers14, 6109 (2022). https://doi.org/10.3390/cancers14246109

  6. Hollin, T. et al. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nat. Commun. 15, 1365 (2024). https://doi.org/10.1038/s41467-024-45519-1

  7. Brenes-Álvarez, M. et al. R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning. Nucleic Acids Res. gkae1247 (2024). https://doi.org/10.1093/nar/gkae1247

  8. Hemm, L. et al. RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets. bioRxiv 2024.09.30.615781 (2024) https://doi.org/10.1101/2024.09.30.615781

  9. Rajagopal, V. et al. An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. Nat Commun:16, 2325 (2025). https://doi.org/10.1038/s41467-025-57671-3

  10. Wäber, N. B. et al. A census of RNA-dependent proteins in yeast. bioRxiv 2024.12.06.627129 (2024). https://doi.org/10.1101/2024.12.06.627129

 

Publications using our R-DeeP methodology

  1. Huppertz, I. et al. Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation. Mol Cell (2022). https://doi.org/10.1016/j.molcel.2022.05.019https://doi.org/10.1016/j.molcel.2022.05.019

  2. Rass, R. A. et al. Inferring Protein Function in an Emerging Virus: Detection of the Nucleoprotein in Tilapia Lake Virus. J Virol (2022). https://doi.org/10.1128/jvi.01757-21

  3. Gokhale, N. S. et al. Cellular RNA interacts with MAVS to promote antiviral signaling. Science 386, eadl0429 (2024). https://doi.org/10.1126/science.adl0429

 

Publications using graphics from our R-DeeP database

  1. McCarthy R. L. et al. Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements. Nat Cell Biol (2022). https://doi.org/10.1038/s41556-021-00725-7

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