HPF1/C4orf27 Is a PARP-1-Interacting Protein that Regulates PARP-1 ADP-Ribosylation Activity

Abstract

We report the identification of histone PARylation factor 1 (HPF1; also known as C4orf27) as a regulator of ADP-ribosylation signaling in the DNA damage response. HPF1/C4orf27 forms a robust protein complex with PARP-1 in cells and is recruited to DNA lesions in a PARP-1-dependent manner, but independently of PARP-1 catalytic ADP-ribosylation activity. Functionally, HPF1 promotes PARP-1-dependent in trans ADP-ribosylation of histones and limits DNA damage-induced hyper-automodification of PARP-1. Human cells lacking HPF1 exhibit sensitivity to DNA damaging agents and PARP inhibition, thereby suggesting an important role for HPF1 in genome maintenance and regulating the efficacy of PARP inhibitors. Collectively, our results demonstrate how a fundamental step in PARP-1-dependent ADP-ribosylation signaling is regulated and suggest that HPF1 functions at the crossroads of histone ADP-ribosylation and PARP-1 automodification.

Graphical abstract

Figure 1

C4orf27/HPF1 Is a PARP-1-Interacting Factor in the DNA Damage Response (A) Selected PBZ domain-containing proteins found in the organisms indicated in the table. (B) Domain structure of C4orf27 from selected organisms. Hs, Homo sapiens; Mm, Mus musculis; Rn, Rattus norvegicus; Gg, Gallus gallus; Dr, Danio rerio; Ce, Caenorhabditis elegans; Dm, Drosophila melanogaster. (C) In vitro ³²P-poly(ADP-ribose) binding assay. (D) U2-O-S cells were transfected with YFP-C4orf27, pretreated with DMSO or PARP inhibitor (PARPi), subjected to laser microirradiation, and imaged at the indicated time. (E) Volcano plot summarizing mass spectrometry analysis of FLAG-C4orf27 interactors from n = 3 independent experiments. (F) FLAG-C4orf27 interactors from (E) were analyzed using STRING and visualized using Cytoscape. (G) 293T cells were transfected with FLAG-empty vector, FLAG-C4orf27, or FLAG-APLF. Cells were lysed, subjected to FLAG immunoprecipitation (IP), and analyzed by Ponceau staining of the SDS-PAGE gel. WCE, whole-cell extract. (H) Samples shown in (G) were further analyzed by immunoblotting with the indicated antibodies. See also Figure S1.

Figure 2

C4orf27/HPF1 Recruitment to Chromatin Is PARP-1 Dependent but Independent of PARP-1 Catalytic Activity (A) 293T/C4orf27^−/− cells were transfected with the indicated combinations of FLAG-empty vector, FLAG-PARP-1, FLAG-PARP2, or FLAG-PARP3 together with either Myc-empty vector or Myc-C4orf27, purified with Myc-tag agarose, and analyzed by immunoblotting with the indicated antibodies. (B) 293T or 293T/PARP-1^−/− cells were transfected with FLAG-empty vector, FLAG-C4orf27, or FLAG-APLF, subjected to FLAG immunoprecipitation, and analyzed by immunoblotting with the indicated antibodies. (C) U2OS/PARP-1^+/+ iGFP-C4orf27 or U2OS/PARP-1^−/− iGFP-C4orf27 cells were induced with doxycycline (+DOX) for 24 hr, subjected to laser microirradiation, and imaged by live-cell microscopy at the indicated time. Cells were subsequently fixed and immunostained with γH2AX antibody. Scale bar, 10 μm. (D) Quantification of data shown in (C). Data represent mean ± SEM from three biologically independent experiments. At least 50 cells were quantified in each experiment. (E) U2OS/iGFP-C4orf27 cells were induced with DOX for 24 hr, pretreated with DMSO or PARPi for 1 hr, and then subjected to laser microirradiation and imaged by live-cell microscopy at the indicated time. Scale bar, 10 μm. See also Figure S2.

Figure 3

C4orf27/HPF1 Interacts Directly with PARP-1 (A) 293T cells were transfected with FLAG-empty vector, FLAG-C4orf27, or FLAG-APLF and treated with PARPi or vehicle. Cells were lysed, subjected to FLAG immunoprecipitation, and analyzed by immunoblotting with the indicated antibodies. (B) As for (A) except cells were treated with either vehicle or H₂O₂ (1 μM) for 10 min. (C) 293T/C4orf27^−/− cells were transfected with FLAG-empty vector, FLAG-C4orf27 WT, or deletion mutants Δ1, Δ2, or Δ3, subjected to FLAG immunoprecipitation, and analyzed by immunoblotting with the indicated antibodies. (D) U2-O-S/C4orf27^−/− cells were transfected with YFP-C4orf27 WT or Δ3, subjected to laser microirradiation, and imaged by live-cell microscopy at the indicated time. Scale bar, 10 μm. (E) Recombinant His-C4orf27 was incubated with GST alone or with various GST-PARP-1 fragments. Samples were subjected to GST pull-down, and bound complexes were analyzed by immunoblotting with the indicated antibodies. (F) As in (E) except with either GST-PARP-1 CAT domain or GST-PARP-2 CAT domain. See also Figure S3.

Figure 4

C4orf27/HPF1 Suppresses PARP-1 Hyper-automodification and Promotes Histone ADP-Ribosylation (A) Clonogenic survival of indicated 293T cell lines treated with various doses of methyl methanesulfonate (MMS). Data represent mean ± SEM from two biologically independent experiments using technical triplicates per data point. (B) Clonogenic survival of indicated U2-O-S cell lines treated with various doses of PARPi. Data represent mean ± SEM from three biologically independent experiments using technical triplicates per data point. (C) U2-O-S cells with the indicated genetic backgrounds were treated with H₂O₂ (1 μM) for 10 min, and whole-cell extracts were analyzed by immunoblotting with the indicated antibodies. ADP-ribosylated PARP-1 (PARP-1^ADPr) and histones (Histones^ADPr) are indicated. (D) Recombinant PARP-1 and increasing molarities of recombinant N-His-C4orf27 were incubated with NAD⁺ and DNA. Reaction products were separated by SDS-PAGE and analyzed by immunoblotting with anti-poly(ADP-ribose) antibody. (E) Recombinant PARP-1, N-His-C4orf27 WT, N-His-C4orf27 Y238A/R239A, N-His-C4orf27 Δ3, or APLF was incubated in various combinations with recombinant histone octamer, and reactions were initiated by addition of DNA and ³²P-NAD⁺. Reaction products were analyzed by SDS-PAGE and autoradiography. (F) Similar to (E), except recombinant histone H1 was used. (G) U2-O-S/C4orf27^+/+ iGFP-ALC1 or U2-O-S/C4orf27^−/− iGFP-ALC1 cells were induced with DOX for 24 hr, subjected to laser microirradiation, and imaged at the indicated times. Scale bar, 10 μm. See also Figure S4.