title: Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
abstract: The regulatory networks of the DNA damage response (DDR) encompass many proteins and posttranslational modifications. Here, we use mass spectrometry-based proteomics to analyze the systems-wide response to DNA damage by parallel quantification of the DDR-regulated phosphoproteome, acetylome, and proteome. We show that phosphorylation-dependent signaling networks are regulated more strongly compared to acetylation. Among the phosphorylated proteins identified are many putative substrates of DNA-PK, ATM, and ATR kinases, but a majority of phosphorylated proteins do not share the ATM/ATR/DNA-PK target consensus motif, suggesting an important role of downstream kinases in amplifying DDR signals. We show that the splicing-regulator phosphatase PPM1G is recruited to sites of DNA damage, while the splicing-associated protein THRAP3 is excluded from these regions. Moreover, THRAP3 depletion causes cellular hypersensitivity to DNA-damaging agents. Collectively, these data broaden our knowledge of DNA damage signaling networks and highlight an important link between RNA metabolism and DNA repair.
authors.affiliation: The NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
authors.forename: Petra
authors.initials: P
authors.lastname: Beli
authors.forename: Natalia
authors.initials: N
authors.lastname: Lukashchuk
authors.forename: Sebastian A
authors.initials: SA
authors.lastname: Wagner
authors.forename: Brian T
authors.initials: BT
authors.lastname: Weinert
authors.forename: Jesper V
authors.initials: JV
authors.lastname: Olsen
authors.forename: Linda
authors.initials: L
authors.lastname: Baskcomb
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Jackson
authors.forename: Chunaram
authors.initials: C
authors.lastname: Choudhary
mesh_terms: D045744:Cell Line, Tumor; D004249:DNA Damage; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D006367:HeLa Cells; D006801:Humans; D010749:Phosphoprotein Phosphatases / Q000502:physiology; D010766:Phosphorylation; D000071636:Protein Phosphatase 2C; D040901:Proteomics; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; C475774:THRAP3 protein, human; D014157:Transcription Factors; D014409:Tumor Necrosis Factor-alpha; C000607460:PPM1G protein, human; D010749:Phosphoprotein Phosphatases; D000071636:Protein Phosphatase 2C