Supplementary Figure 1

Supplementary Figure 1 a γ-h2ax MDC1 RNF8 FK2 BRCA1 U2OS Cells sgrna-1 ** 60 sgrna 40 20 0 % positive Cells (>5 foci per cell) b ** 80 sgrna sgrna γ-h2ax MDC1 γ-h2ax RNF8 FK2 MDC1 BRCA1 RNF8 FK2 BRCA1 HeLa Cells sgrna-1 sgrna sgrna ** ** 60 sgrna 40 20 0 γ-h2ax MDC1 RNF8 FK2 BRCA1 80 % positive Cells (>5 foci per cell)

Supplementary Figure 1. regulates -BRCA1 foci formation in response to cisplatin. (a-b) Control or knockout U2OS (a) or HeLa (b) cells were treated with cisplatin and foci formation of the indicated factors were detected by immunofluorescence with indicated antibodies. Representative images are shown in the upper panels. Scale bar, 10 μm. Quantification of the percentage of cells displaying foci formation is shown in the lower left panels. expression in these cells were examined by western blot and is shown in the lower right panel. Error bars represent SEM from three independent experiments. **P < 0.01. >200 cells were counted per experiment. Statistical analyses were performed with the ANOVA.

Supplementary Figure 2 a γ-h2ax BRCA1 CCDC98 % positive Cells (>5 foci per cell) sgrna sgrna Olaparib c 80 γ-h2ax MDC1 BRCA1 sgrna 20 γ-h2ax b sgrna: sgrna 10uM d sgrna sgrna 0 1 2 0 1 2 (hrs) 1uM sgrna H3 I-SceI BRCA1 MERIT 40 Ƴ-H2AX CCDC98 CCDC98 BRCA1 Chromatin BRCA1 10uM ** ** 40 IR: 1uM sgrna 60 0 IR treated (2Gy) sgrna ** Merge 2 37 10

Supplementary Figure 2. regulates BRCA1-A complex recruitment to DSBs. (a) Control or knockout EFO-27 cells were treated with IR (2Gy) and foci formation of the indicated factors were detected by immunofluorescence with indicated antibodies. Representative images are shown in the left panels. Quantification of the percentage of cells displaying foci formation is shown in the right panels. Scale bar, 10 μm. Error bars represent SEM from three independent experiments. **P < 0.01. >200 cells were counted per experiment. Statistical analyses were performed with the ANOVA. (b) Control or knockout EFO-27 cells were treated with IR (2Gy). Whole cell lysates and chromatin fractions were prepared and blotted with the indicated antibodies. (c) Control or knockout EFO-27 cells were treated with olaparib at indicated concentrations for 6 hr. Foci formation of the indicated factors was detected by immunofluorescence with indicated antibodies. Scale bar, 10 μm. (d) Colocalization of BRCA1 with γ-h2ax at DSB site created by I-SceI was examined in control or knockout cells. Scale bar, 10 μm. expression in these cells was examined by western blot and is shown in the panel to the left.

Supplementary Figure 3 a 0 5 10 15 20 60 120 180 300 (sec) GFP- GFP- b Relative fluorescence intensity 4 3 2 1 0 GFP- GFP- 0 60 120 180 240 300 (s)

Supplementary Figure 3. Recruitment kinetics of and. (a-b) Cells expressing GFP- or GFP- were subjected to laser microirradiation. Laser stripes were examined at the indicated time points. Scale bar, 10 μm. The intensity of each laser stripe at each time point was determined by averaging values from 10 cells and is graphed in (b).

Supplementarg Figure 4 a sgrna: HA- - - WT CA b sgrna: HA- - - WT CA d IP: IgG sgrna: anti-ub HeLa c γ-h2ax WT CA sgrna-1 2 1 IP: Lysate % positive Cells (>5 foci per cell) anti-ub U2OS 120 sgrna+ WT 80 60 40 20 0 γ-h2ax sgrna+ CA ** 2 1 IP: Lysate BRCA1 CCDC98 MERIT 40 anti-ub BRCA1 CCDC98 MERIT 40 2 37 2 1 2 37 IP Input

Supplementary Figure 4. Deubiquitination of by affects foci formation but not BRCA1-A complex stabilization. (a-b) HeLa (a) or U2OS (b) cells stably expressing control, sgrna, or sgrna with the indicated constructs, were lysed under denaturing conditions and was immunoprecipitated. Blots were probed with the indicated antibodies. (c) EFO-27 cells stably expressing sgrna with the indicated constructs were treated with cisplatin and foci formation of the indicated factors were detected by immunofluorescence with indicated antibodies. Representative images are shown in the left panel. Scale bar, 10 μm. Quantification of the percentage of cells displaying foci formation is shown in the right panel. Error bars represent SEM from three independent experiments. **P < 0.01. >200 cells were counted per experiment. Statistical analyses were performed with the Student s t-test. (d) Cell lysates from control () or knockout EFO-27 cells were subjected to immunoprecipitation with control IgG or antibodies. The western blots were then blotted with the indicated antibodies.

Supplementary Figure 5 a 0Gy 2Gy d 0Gy 2Gy sgrna sgrna sgrna sgrna sgrna + WT sgrna sgrna + CA sgrna + sgrna sgrna: - + - + sgrna : - - + + b c Surivival Fraction (%) 10 sgrna sgrna sgrna+ WT Surivival Fraction (%) 10 sgrna sgrna sgrna+ WT 1 IR: sgrna+ CA 0 1 2 4 8 HeLa (Gy) 1 IR: sgrna+ CA 0 1 2 4 8 U2OS (Gy)

Supplementary Figure 5. regulates G2/M checkpoint and radiosensitivity. (a) The representative data for Fig 3a. Scale bar, 0 μm. (b-c) HeLa (b) or U2OS (c) cells stably expressing control, sgrna, or sgrna with the indicated constructs were generated. Sensitivity of these cells to IR was assessed using colony formation assay. Error bars represent SEM from three independent experiments. (d) The representative data for Fig 3d. Scale bar, 0 μm. and expression in these cells were examined by western blot and is shown in the lower panel.

Supplementary Figure 6 sgrna sgrna a Homologous Recombination (Normalize to 1) 1.4 1.2 1 0.8 0.6 0.4 0.2 0 HA- - - WT CA sgrna: HA- - - WT CA sgrna: sgrna+wt sgrna+ca b Homologous Recombination (Normalize to 1) 1.2 1 0.8 0.6 0.4 0.2 0 Spautin-1: - + - + sgrna: Spautin-1: - + - + n.s. sgrna: - sgrna Spautin-1 sgrna+spautin-1

Supplementary Figure 6. regulates HR. (a) HR-mediated DSB repair capacity of control, knockout, and knockout cells stably expressing the indicated constructs were assessed using a reporter system. (b) HR-mediated DSB repair capacity of control and knockout cells treated with or without Spautin-1 was assessed using a reporter system. Error bars represent SEM from three independent experiments. *P < 0.05. Statistical analyses were performed with the ANOVA.

Supplementary Figure 7 a sgrna: Olaparib: anti-ub b HA- - 1 10-1 10 (um) WT 5KR-1 (K20/31/75/90/112R) 2 1 5KR-2 (K5146/232/245/374/382R) 5KR-3 (K544/567/587/607/635R) IP: Lysate c HA- sgrna: anti-ub HA WT 2KR (K20/31R) 3KR (K75/90/112R) d HA- WT 2 1 K75R IP:FLAG Lysate K90R e GST--WT GST--3KR His-K48 Ub chain His-K63 Ub chain K112R anti-his 3KR (K75/90/112R) GST GST + + - - - + + + + 37 2 1 70 37 20 37 His-pulldown Input sgrna: sgrna: anti-ub 2 1 IP:FLAG anti-ub 2 1 IP:FLAG HA Lysate HA Lysate

Supplementary Figure 7. Identification of the deubiquitination sites targeted by. (a) Control and knockout cells treated with olaparib at different concentrations were lysed under denaturing conditions and was immunoprecipitated. Blots were probed with the indicated antibodies. (b-d) Control and knockout cells were transfected with indicated constructs. Cells were lysed under denaturing conditions and HA- was immunoprecipitated. Blots were probed with the indicated antibodies. (e) GST- WT and 3KR mutant proteins were subjected to pull down assay by incubating with indicated His-Ub chains conjugated with Ni-NTA beads. After washing, proteins bound on beads were subjected to western blot with indicated antibodies.

Supplementary Figure 8 cisplatin p-sq/tq e a % positive Cells (>5 foci per cell) 80 60 40 20 0 - + + + HeLa Ku55933 phosphatase IP: b cisplatin - + + + p-sq/tq U2OS Ku55933 phosphatase sgrna sgrna sgrna+ WT sgrna+ T196A 0 γ-h2ax CCDC98 HA- - - WT T196A BRCA1 sgrna: IP: c HA- cisplatin p-t196 HA f Homologous Recombination (Normalize to 1) 1.2 1 0.8 0.6 0.4 0.2 WT T196A - + - + sgrna: d HA- - - WT TA cisplatin + + + + IP:HA anti-ub 2 1 IP: Lysate sgrna: HA- - - WT T196A g sgrna sgrna sgrna+wt sgrna+t196a MDC1 shrna h i MDC1 Ƴ-H2AX I-SceI Merge 2 Surivival Fraction (%) 10 1 Olaparib: sgrna sgrna sgrna+wt sgrna+ T196A 0 0.1 0.2 0.5 1 2 (um) shrna MDC1 shrna

Supplementary Figure 8. Phosphorylation of regulates DDR. (a-b) HeLa (a) or U2OS (b) cells were pretreated with DMSO or 25μM Ku55933 for 2 hrs following which they were left untreated or treated with cisplatin. After an additional 1 hr, was immunoprecipitated, left untreated or treated with phosphatase, and immunoblotted with phospho-sq/tq (psq/tq) antibody. (c) HEK293T cells transfected with HA- WT or T196A mutant were left untreated or treated with cisplatin. HA- was immunoprecipitated and immunoblotted with T196 phospho-specific antibody. (d) Control and knockout cells were transfected with the indicated constructs. Cells were lysed under denaturing conditions and was immunoprecipitated. Blots were probed with the indicated antibodies. (e) EFO- 27 cells stably expressing, sgrna or sgrna with the indicated constructs were treated with cisplatin and foci formation of the indicated factors were detected by immunofluorescence with the indicated antibodies. Error bars represent SEM from three independent experiments. >200 cells were counted per experiment. (f-g) Control, knockout, and knockout cells stably expressing the indicated constructs were subjected to DR-GFP based HR assay. Error bars represent SEM from three independent experiments. **P < 0.01, *P<0.05. Statistical analyses were performed with the ANOVA. expression is shown in the right panel. The representative FACS data is shown in (g). (h) Control, knockout, and knockout cells stably expressing the indicated constructs were subjected to colony formation assay to assess the sensitivity of cells to olaparib. Error bars represent SEM from three independent experiments. (i) Co-localization of with γ-h2ax at DSB site created by I-SceI was examined in control or MDC1 knockdown cells. Scale bar, 5 μm. MDC1 expression in these cells was examined by western blot and is shown in the right upper panel.

Supplementary Figure 9 a log2 copy number units 1.0 0.5 0.0-0.5-1.0-1.5 log2 copy number units 1.0 0.5 0.0-0.5-1.0-1.5 CCDC98 log2 copy number units 1.0 0.5 0.0-0.5-1.0-1.5 BRCA1 Normal (561 cases) Ovarian carcinoma (607 cases) Normal (561 cases) Ovarian carcinoma (607 cases) Normal (561 cases) Ovarian carcinoma (607 cases) log2 copy number units 3.0 2.0 1.0 0.0-1.0 MERIT40 log2 copy number units 1.5 1.0 0.5 0.0-0.5-1.0 BRCC45 b Normal (561 cases) Ovarian carcinoma (607 cases) Normal (561 cases) Ovarian carcinoma (607 cases)

Supplementary Figure 9. The expression of in ovarian cancer. (a) The expression of BRCA1-A complex in normal and ovarian carcinoma (Oncomine data). (b) Gene copy-number and mutation data of and BRCA1-A complex in ovarian cancer (TCGA data).

Supplementary Figure 10 a HOSE EFO-27 SKOV-3 FU-OV-1 OVCAR-3 A2780 b HOSE EFO-27 SKOV-3 FU-OV-1 OVCAR-3 A2780 2 PTEN anti-ub 1 c Survival Fraction (%) 10 shrna USP10 shrna shrna shrna+spautin-1 USP10 shrna+spautin-1 shrna+spautin-1 1 Olaparib: 0 0.1 0.2 0.5 1 2 (um) d Absorbance (590nm) (Normalize day 1 to 1) 14 12 10 8 6 4 2 0 ctrl sgrna sgrna-1 sgrna-2 1 2 3 4 5 6 (Days) e 0 800 Cell Number 600 400 sgrna sgrna-1 sgrna-2 G1:43.9 S: 47.19 G2/M: 8.91 G1:44.12 S: 46.19 G2/M: 9.69 G1:42.9 S: 46.14 G2/M: 10.96 200 0 Channels (PI-A)

Supplementary Figure 10. regulates chemoresistance in ovarian cancer. (a) The human ovarian epithelial cell line (HOSE) and ovarian carcinoma cell lines were lysed under denaturing conditions and was immunoprecipitated. Blots were probed with the indicated antibodies. (b) Expression of PTEN in human ovarian epithelial cell line and ovarian carcinoma cell lines. (c) Control, knockdown, and USP10 knockdown cells were subjected to colony formation assay to assess the sensitivity of cells to olaparib or olaparib with spautin-1. (d) Growth curves of EFO-27 cells stably expressed ctrl or sgrnas were measured by MTS assay. (c-d) Error bars represent SEM from three independent experiments. (e) Cell cycle profile of EFO-27 cell stably expressed ctrl or sgrnas.

Supplementary Figure 11 Fig 1b sgrna -1-2 Fig 2a IP IgG Input IgG Fig 2b Fig 2c sgrna: IP: IgG IgG sgrna: HA- - - WT CA IP: Ub blot Fig 2d sgrna: Spautin-1: - + - + Fig 2e IP: - WT CA HA- Ub blot His-Ub blot GST- Fig 2f His-Ub: - K48 K63 K63R 13sgRNA: - + - + - + - + IP: His-Ub blot His-Ub Input

Supplementary Figure 11. Original scan of the blots presented in the main text. Related to Figure 1 and 2.

Supplementary Figure 12 Fig 4a sgrna: Cisplatin: - + - + IP: Fig 4b sgrna: Ub chain K48 K63 Cisplatin: + - + - + Ub Blot His-Ub pulldown Input Fig 4d HA- WT 3KR Fig 4f sgrna: sgrna: Ub chain K48 K63 HA-: WT WT 3KR WT 3KR IP:HA- HA- Input His-Ub pulldown Ub Blot HA- Fig 5a cisplatin - + + + Ku55933 phosphatase Fig 5b HA- WT T196A T380A T385A cisplatin - + - + - + - + p-sq/tq p-sq/tq IP: IP:HA-

Supplementary Figure 12. Original scan of the blots presented in the main text. Related to Figure 4 and 5.

Supplementary Figure 13 Fig 5c ATM+/+ ATM-/- - IR Cisplatin - IR Cisplatin Fig 5d WT T196A HA Fig 5f cisplatin: - - + HA-MDC1 - + + Input ATM IP:HA-MDC1 p-sq/tq Fig 5h HA-: WT T196A Cisplatin: + - + - + HA- HA- Input IP: Fig 5g MDC1-FHA GST GST-pulldown Fig 5i Conjugated Peptides Fig 6f T196 p-t196 Input HA-MDC1: - WT D1 D2 D3 D4 D5 D6 D7 D8 GST HA- IP:HA-MDC1 Fig 6b Incubated with GST-MDC1 -FHA HOSE EFO-27 SKOV-3 FU-OV-1 OVCAR-3 A2780 Input

Supplementary Figure 13. Original scan of the blots presented in the main text. Related to Figure 5 and 6.