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@ARTICLE{Rajagopal:186468,
      author       = {V. Rajagopal$^*$ and A.-S. Loubal$^*$ and N. Engel$^*$ and
                      E. Wassmer$^*$ and J. Seiler$^*$ and O. Schilling$^*$ and M.
                      Caudron-Herger$^*$ and S. Diederichs$^*$},
      title        = {{P}roteome-{W}ide {I}dentification of {RNA}-{D}ependent
                      {P}roteins in {L}ung {C}ancer {C}ells.},
      journal      = {Cancers},
      volume       = {14},
      number       = {24},
      issn         = {2072-6694},
      address      = {Basel},
      publisher    = {MDPI},
      reportid     = {DKFZ-2022-03189},
      pages        = {6109},
      year         = {2022},
      note         = {#EA:B150#LA:B150#},
      abstract     = {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.},
      keywords     = {R-DeeP (Other) / RNA (Other) / RNA-binding proteins (Other)
                      / RNA-dependent proteins (Other) / Sucrose density gradients
                      (Other)},
      cin          = {B150 / FR01},
      ddc          = {610},
      cid          = {I:(DE-He78)B150-20160331 / I:(DE-He78)FR01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36551595},
      pmc          = {pmc:PMC9776756},
      doi          = {10.3390/cancers14246109},
      url          = {https://inrepo02.dkfz.de/record/186468},
}