Splicing controls the ubiquitin response during DNA double-strand break repair

Abstract

Although evidence that splicing regulates DNA repair is accumulating, the underlying mechanism(s) remain unclear. Here, we report that short-term inhibition of pre-mRNA splicing by spliceosomal inhibitors impairs cellular repair of DNA double-strand breaks. Indeed, interference with splicing as little as 1 h prior to irradiation reduced ubiquitylation of damaged chromatin and impaired recruitment of the repair factors WRAP53β, RNF168, 53BP1, BRCA1 and RAD51 to sites of DNA damage. Consequently, splicing-deficient cells exhibited significant numbers of residual γH2AX foci, as would be expected if DNA repair is defective. Furthermore, we show that this is due to downregulation of the E3 ubiquitin ligase RNF8 and that re-introduction of this protein into splicing-deficient cells restores ubiquitylation at sites of DNA damage, accumulation of downstream factors and subsequent repair. Moreover, downregulation of RNF8 explains the defective repair associated with knockdown of various splicing factors in recent genome-wide siRNA screens and, significantly, overexpression of RNF8 counteracts this defect. These discoveries reveal a mechanism that may not only explain how splicing regulates repair of double-strand breaks, but also may underlie various diseases caused by deregulation of splicing factors, including cancer.

Figure 1

Recruitment of DNA repair factors to double-strand breaks is impaired in splicing-deficient cells. (a) HeLa Luc-I or Luc cells were exposed to DMSO (control), 100 nM pladienolide B or 50 μM isoginkgetin for 1–16 h. After normalization to the corresponding DMSO value, the ratio between Luc-I and Luc luciferase activity is presented as a percentage. Means±S.D. are shown, n=4. (b) U2OS cells were treated with pladienolide B or isoginkgetin for 2, 6 or 16 h, irradiated (6 Gy, 1 h recovery) 1 h prior to termination of the treatment, fixed and immunostained for γH2AX, MDC1, WRAP53β, RNF168, conjugated ubiquitin recognized by the FK2 antibody, 53BP1, RAD51 or BRCA1. Nuclei were stained with DAPI in all immunofluorescence experiments. The numbers in white represent the percentage of 100–200 cells counted whose nuclei contained >10 IR-induced foci. Means±S.D. are shown, n=3. *P-value<0.05, as determined by a non-paired two-tailed Student's t-test. The ‘foci-like' accumulations RAD51 after splicing inhibition in (b) are not IR-induced foci, but accumulation of RAD51 in the nucleolus for unknown reasons

Figure 2

Inhibition of splicing downregulates repair factors at both the mRNA and protein levels. (a) U2OS cells were treated with pladienolide B for 2, 6 and 16 h and irradiated (6 Gy, 1 h recovery) 1 h prior to termination of the treatment. The levels of the indicated mRNAs were measured through qPCR analysis. The change is relative to the DMSO control and two reference genes (18S rRNA and β-actin). Means±S.D. are shown, n=3. (b) qPCR analysis of the levels mRNA and pre-mRNA for RNF8 and RAD51 in U2OS cells treated with pladienolide B or isoginkgetin for 2, 6 or 16 h and irradiated (6 Gy, 1 h recovery) 1 h prior to termination of this treatment. The change is expressed relative to the DMSO control value and the levels of mRNA for two reference genes (18S rRNA and β-actin). Means±S.D. are shown, n=3. The arrows indicate the positioning of the PCR primers used and their sequences are shown in Supplementary Table S1. (c) Western blotting following pladienolide B treatment of U2OS cells as described in (a). β-Actin was used as a loading control. Densitometric quantification of each protein is shown in Supplementary Figure S2B. The three MDC1 bands correspond to the unphosphorylated, phosphorylated and hyperphosphorylated forms of full-length MDC1

Figure 3

Overexpression of RNF8 restores repair of DNA double-strand breaks in splicing-deficient cells. (a) U2OS cells were treated with DMSO, pladienolide B or isoginkgetin for 16 h, irradiated (6 Gy, 1 h recovery) 1 h prior to termination of this treatment, and then subjected to western blotting for H2A, RNF8 and β-actin. (b and c) U2OS cells were transfected with either GFP-RNF8 or GFP-Empty for 2 h, followed by addition of pladienolide B, isoginkgetin or DMSO, incubation for an additional 5 h, irradiation with 6 Gy, fixation 1 h later, and immunostaining for (b) conjugated ubiquitin (FK2 antibody) and (c) 53BP1. The numbers in white indicate the percentage of 100 transfected, i.e, green cells whose nuclei contained >10 IR-induced foci. Means±S.D. are shown, n=3. (d) U2OS cells were treated as above, except that fixation was performed 24 h after irradiation and the immunostaining was for γH2AX. Again, the white numbers indicate the percentage of 100 transfected, i.e, green cells whose nuclei contained >10 γH2AX foci. Means±S.D. are shown, n=3. (e) The efficiency of HR measured in direct repeated-GFP U2OS cells transfected with I-SceI in combination with either Flag-Empty or Flag-RNF8 for 24 h, followed by addition of DMSO or pladienolide B and incubation for another 24 h. Means±S.D. are shown, n=3. *P<0.05, as determined by a non-paired two-tailed Student's t-test

Figure 4

When splicing-related factors are depleted, overexpression of RNF8 restores repair of DNA double-strand breaks. (a) Western blotting of SF3B1, RBMX, PRPF8 and RNF8 in U2OS cells treated for 48 h with the siRNAs indicated. β-Actin was used as a loading control. (b) U2OS cells were transfected with the siRNAs indicated for 48 h, exposed to IR (6 Gy), and 1 h later, immunostained for γH2AX and conjugated ubiquitin (with the FK2 antibody). (c) U2OS cells were treated with the siRNAs indicated for 40 h, followed by transfection with either GFP-RNF8 or GFP-Empty plasmid for 7 h; exposure to IR (6 Gy) and fixation 1 h later and immunostaining for conjugated ubiquitin. The white numbers indicate the percentage of 100 transfected cells, i.e, green cells whose nuclei contained >10 IR-induced foci. Means±S.D. are shown, n=3. *P<0.05, as determined by a non-paired two-tailed Student's t-test. (d) Schematic model of how splicing regulates repair of DNA double-strand breaks