TY  - JOUR
AU  - Rajagopal, Varshni
AU  - Loubal, Astrid-Solveig
AU  - Engel, Niklas
AU  - Wassmer, Elsa
AU  - Seiler, Jeanette
AU  - Schilling, Oliver
AU  - Caudron-Herger, Maiwen
AU  - Diederichs, Sven
TI  - Proteome-Wide Identification of RNA-Dependent Proteins in Lung Cancer Cells.
JO  - Cancers
VL  - 14
IS  - 24
SN  - 2072-6694
CY  - Basel
PB  - MDPI
M1  - DKFZ-2022-03189
SP  - 6109
PY  - 2022
N1  - #EA:B150#LA:B150#
AB  - Following the concept of RNA dependence and exploiting its application in the R-DeeP screening approach, we have identified RNA-dependent proteins in A549 lung adenocarcinoma cells. RNA-dependent proteins are defined as proteins whose interactome depends on RNA and thus entails RNA-binding proteins (RBPs) as well as proteins in ribonucleoprotein complexes (RNPs) without direct RNA interaction. With this proteome-wide technique based on sucrose density gradient ultracentrifugation and fractionation followed by quantitative mass spectrometry and bioinformatic analysis, we have identified 1189 RNA-dependent proteins including 170 proteins which had never been linked to RNA before. R-DeeP provides quantitative information on the fraction of a protein being RNA-dependent as well as it allows the reconstruction of protein complexes based on co-segregation. The RNA dependence of three newly identified RNA-dependent proteins, DOCK5, ELMO2, also known as CED12A, and ABRAXAS1, also known as CCDC98, was validated using western blot analysis, and the direct RNA interaction was verified by iCLIP2 for the migration-related protein DOCK5 and the mitosis-related protein ABRAXAS1. The R-DeeP 2.0 database provides proteome-wide and cell line-specific information from A549 and HeLa S3 cells on proteins and their RNA dependence to contribute to understanding the functional role of RNA and RNA-binding proteins in cancer cells.
KW  - R-DeeP (Other)
KW  - RNA (Other)
KW  - RNA-binding proteins (Other)
KW  - RNA-dependent proteins (Other)
KW  - Sucrose density gradients (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:36551595
C2  - pmc:PMC9776756
DO  - DOI:10.3390/cancers14246109
UR  - https://inrepo02.dkfz.de/record/186468
ER  -