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Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation

An Author Correction to this article was published on 09 April 2018

This article has been updated

Abstract

Histone methylation regulates DNA repair. However, the mechanisms that underlie the regulation of histone methylation during this repair remain to be further defined. Here, we show that exposure to ionizing radiation induces DNA-PK-dependent phosphorylation of nuclear fumarase at Thr 236, which leads to an interaction between fumarase and the histone variant H2A.Z at DNA double-strand break (DSB) regions. Locally generated fumarate inhibits KDM2B histone demethylase activity, resulting in enhanced dimethylation of histone H3 Lys 36; in turn, this increases the accumulation of the Ku70-containing DNA-PK at DSB regions for non-homologous end-joining DNA repair and cell survival. These findings reveal a feedback mechanism that underlies DNA-PK regulation by chromatin-associated fumarase and an instrumental function of fumarase in regulating histone H3 methylation and DNA repair.

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Figure 1: H2A.Z-regulated recruitment of FH to DSB regions promotes the accumulation of Ku70 at DSB regions.
Figure 2: DNA-PK phosphorylates FH at Thr 236 and subsequently promotes Ku70 accumulation at DSB regions and NHEJ.
Figure 3: DNA-PK-phosphorylated FH promotes the DNA-PK complex accumulation at DSB regions and NHEJ.
Figure 4: The binding of FH pThr-236 to H2A.Z promotes the DNA-PK complex accumulation at DSB regions and NHEJ.
Figure 5: Fumarate produced by chromatin-associated FH promotes NHEJ.
Figure 6: Fumarate produced by chromatin-associated FH inhibits KDM2B-mediated H3K36me2 demethylation.
Figure 7: Fumarate produced by chromatin-associated FH promotes cell survival.
Figure 8: A schematic model showing that DNA-PK-mediated phosphorylation of fumarase promotes DNA repair by local fumarate-inhibited histone H3 demethylation.

Change history

  • 09 April 2018

    In the version of this Article originally published, the authors mistakenly used the same images for three different time points in Fig. 2d: images for 24 h post-IR WT were also used for 0 h post-IR WT (top row, left panels) and for 1 h post-IR, T236A mutant (2nd row from the top, right panels). The correct images from these experiments have now been inserted in the figure in all online versions of the Article. In addition, results from this experiment and from two additional independent experiments have been uploaded to Figshare and the sentence 'Additional repeats of this experiment have been uploaded to Figshare28.' has been added to the figure legend to highlight this fact. The Figshare doi has been added as reference 28. The new reference and corrected Fig. 2d are shown below. 28. Jiang, Y. et al. FH pT236-gammaH2AX-1-2-3.tif. Figshare https://doi.org/10.6084/m9.figshare.5867907 (2018).

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Acknowledgements

We thank D. Hawke, B.-F. Pan and M.-B. Hossain at MD Anderson for their technical assistance and A. Sutton for her critical reading of this manuscript. This work was supported by National Cancer Institute grants 2R01CA109035 (Z.L.) and 1R0CA169603 (Z.L.), National Institute of Neurological Disorders and Stroke grant 1R01NS089754 (Z.L.), the MD Anderson Cancer Center Support Grant CA016672, James S. McDonnell Foundation 21st Century Science Initiative in Brain Cancer Research Award 220020318 (Z.L.), 2P50CA127001 (Brain Cancer SPORE), a Sister Institution Network Fund from The University of Texas MD Anderson Cancer Center (Z.L.), and the Odyssey Fellowship from MD Anderson (Y.J.). Z.L. is a R. E. Rutherford Distinguished Professor.

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Authors and Affiliations

Authors

Contributions

This study was conceived by Z.L.; Z.L. and Y.J. designed the study; Y.J., X.Q., J.S., Y.W., X.L., R.L. and Y.X. performed experiments; Q.C., G.P. and S.-Y.L. provided reagents and conceptual advice; Z.L. wrote the paper with comments from all authors.

Corresponding author

Correspondence to Zhimin Lu.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 IR induces the association of FH with chromatin.

(a) U2OS cells synchronized by thymidine double block (2 mM) underwent no release (G1 phase) or release for 2 h (S phase) or 6 h (G2 phase). These cells were then exposed to IR (10 Gy) and analysed by an immunoblotting assay with the indicated antibodies and flow cytometry. Data represent one out of 3 experiments. (b) GSC11 cells that were synchronized by thymidine double block (2 mM) were not released (G1 phase) or were released for 2 h (S phase) or 6 h (G2 phase). These cells then underwent IR (10 Gy) and were harvested at the indicated time points. Chromatin extracts were prepared. CENP-A was used as a control for chromatin-associated proteins. Immunoblotting analyses were performed with the indicated antibodies. Data represent one out of 3 experiments. (c) Thymidine double block-synchronized U2OS cells expressing Flag-FH were exposed to IR (10 Gy). Chromatin extracts were subjected to immunoprecipitation with an anti-FH antibody and analysed by mass spectrometry. FH-interacting histone proteins in the cells with or without IR identified by mass spectrometry were shown.

Supplementary Figure 2 DNA-PK phosphorylates FH at T236.

Data represent one out of 3 experiments unless specifically indicated. (a) In vitro phosphorylation analyses were performed by mixing the purified DNA-PK complex with bacterially purified His-FH in the presence of [γ-32P]ATP. Immunoblotting analyses were performed with the indicated antibodies. (b) The specificity of this FH pT236 antibody was validated using a specific phosphorylation-blocking peptide. In vitro phosphorylation analyses were performed by mixing the purified DNA-PK complex with bacterially purified His-FH. Immunoblotting analyses were performed with the indicated antibodies in the presence or absence of a phospho-specific blocking peptide for the FH pT236 antibody. (c) Thymidine double block-synchronized U2OS cells, pretreated with or without NU7441 (1 μM) or KU55933 (10 μM) underwent IR (10 Gy). Immunoblotting analyses were performed with the indicated antibodies. (d) U2OS cells were harvested 1 h after IR (10 Gy). The cytosolic and nuclear fractions and chromatin-associated proteins were prepared. The FH expression in each fraction was quantified and normalized by actin levels in harvested cells (left panel). The nuclear fractions of IR-treated cells were immuno-depleted by normal IgG or an anti-FH pT236 antibody and immunoblotted with the indicated antibodies (right panel). CE: chromatin extract; NE: nuclear extract; Cy: cytosol. (e) U2OS cells with depleted endogenous FH and reconstituted expression of the indicated FH proteins were irradiated with IR (3 Gy). Immunofluorescence analyses with the indicated antibodies were performed at 1 h after IR. Bar, 10 μM. (f) U2OS cells with or without depleted endogenous FH and reconstituted expression of the indicated FH proteins were irradiated with IR (10 Gy) and harvested at the indicated time points. Immunoblotting analyses were performed with the indicated antibodies.

Supplementary Figure 3 DNA-PK-phosphorylated FH promotes the DNA-PK complex accumulation at DSB regions and NHEJ.

(a,b,c) Immunoblotting analyses were performed with the indicated antibodies. (a) U2OS cells were expressed with a vector for control shRNA or FH shRNA and reconstituted with expression of rFH (N) and rFH (N) T236A (left panel) or rFH at full length (right panel). rFH (FL) underwent a N-terminal cleavage in mitochondria and was redistributed in mitochondria and cytosol. (b,c) Thymidine double block-synchronized U2OS cells with depleted endogenous FH and reconstituted expression of the indicated FH proteins were exposed to IR (10 Gy) and harvested 1 h after IR. The chromatin extracts were prepared. (d) A schematic of NHEJ and HR repair at the DR-GFP locus, which is described in Material and Method section. (e) DR-GFP-expressed U2OS cells with depleted Ku70 expressed or did not express I-SceI. PCR analyses for NHEJ were performed 42 h after transfection. A representative image of PCR products digested by I-SceI and BcgI is shown (left panel). The data represent the mean ± SD (n = 3 independent experiments, right panel). stands for P < 0.05 between the cells with or without expressing Ku70 shRNA. (f) A schematic of the efficiency of I-SceI-dependent cleavage at the DR-GFP locus, which is described in Material and Methods. (g,h) DR-GFP-expressed U2OS cells with FH depletion and with or without reconstituted expression of WT rFH (N) or rFH (N) T236A expressed or did not express I-SceI. (g) PCR analyses for I-SceI-uncut SceGFP were performed 42 h after transfection, as described in Supplementary Fig. 2f. Representative images of PCR products were shown (left panel). The data represent the mean ± SD (n = 3 independent experiments, right panel). Comparable amount of 0.65 Kb PCR products suggested that the efficiency of DSB production by I-Sce1 in each cell line is similar to each other. (h) Flow cytometry analyses for HR were performed 42 h after transfection (left panel). The data represent the mean ± SD (n = 3 independent experiments, right panel). # stands for no statistical significance between expression of WT rFH(N) and rFH(N) T236A.

Supplementary Figure 4 FH binds to H2A.Z.

(a) U2OS cells were expressed with a vector for control shRNA or H2A.Z shRNA and reconstituted with expression of WT rH2A.Z or rH2A.Z (NKLLG). Immunoblotting analyses were performed with the indicated antibodies. Data represent one out of 3 experiments. (b) DR-GFP-expressing U2OS cells with depleted H2A.Z and reconstituted expression of the indicated H2A.Z proteins were transfected with a vector that expressed I-SceI. ChIP analyses were performed with an anti-Flag antibody at the indicated time points after I-SceI transfection. Data represent one out of 3 experiments. (c) DR-GFP-expressed U2OS cells with H2A.Z depletion and with or without reconstituted expression of WT rH2A.Z or rH2A.Z (NKLLG) were transfected with a vector with or without expressing I-SceI. PCR analyses for I-SceI-uncut SceGFP were performed 42 h after transfection, as described in Supplementary Fig. 2f. Representative images of PCR products were shown (left panel). The data represent the mean ± SD (n = 3 independent experiments, right panel). Comparable amount of 0.65 Kb PCR products suggested that the efficiency of DSB production by I-SceI in each cell line is similar to each other.

Supplementary Figure 5 Fumarate produced by chromatin-associated FH promotes NHEJ.

(a) Chromatin extracts of thymidine double block-synchronized U2OS cells with depleted endogenous FH and reconstituted expression of the indicated FH proteins were collected 1 h after IR. Chromatin extracts were subjected to immunoblotting (left panel) or immunoprecipitation analyses (right panel) with the indicated antibodies. Data represent one out of 3 experiments. (b) U2OS cells were expressed with the indicated FH-Flag proteins. FH-Flag proteins were immunoprecipitated and the relative FH activity was measured. The data represent the mean ± SD (n = 3 independent experiments). (c) Immobilized, purified GST-H2A.Z protein was mixed with the indicated purified His-FH proteins, with or without DNA-PK. A GST pull-down assay was performed. Immunoblotting analyses were performed with the indicated antibodies. Data represent one out of 3 experiments. (d) U2OS cells were incubated with the indicated concentrations of monoethyl-fumarate. The relative abundance of intracellular fumarate was measured. The data represent the mean ± SD (n = 3 independent experiments). (e) DR-GFP-expressing U2OS cells with depleted FH and reconstituted expression of the indicated FH proteins were incubated with malate (5 mM) for 20 h after I-SceI transfection. ChIP analyses were performed with an anti-Ku70 antibody. The data represent the mean ± SD (n = 3 independent experiments). (f) DR-GFP-expressing U2OS cells with depleted FH and reconstituted expression of the indicated FH proteins were incubated with malate (5 mM) for 20 h after I-SceI transfection. An NHEJ analysis was performed. A representative image of the PCR products digested by I-SceI and BcgI is presented. The data represent the mean ± SD (n = 3 independent experiments). (g) U2OS cells, with or without FH depletion, were reconstituted with expression of the indicated FH proteins before being harvested. The relative abundance of intracellular fumarate was measured. The data represent the mean ± SD (n = 3 independent experiments).

Supplementary Figure 6 Fumarate produced by chromatin-associated FH inhibits KDM2B-mediated demethylation at DSB regions.

(ac,f) The data represent the mean ± SD (n = 3 independent experiments). (d,e,g) Data represent one out of 3 experiments. (a,b) U2OS cells were transfected with or without a vector expressing I-SceI. (a) ChIP analyses with antibodies for H3K36me2, H3K9me2, H3K9me3 and H3K27me2 were performed at the indicated time points after I-SceI transfection. (b) ChIP analyses with the indicated histone H3 methylation antibodies were performed 20 h after I-SceI transfection. The primers described in Fig. 1f were used for the PCR. Control primers were selected against a specific region of chromosome 12. The y-axis stands for the value of I-SceI-induced fold increase of binding of the methylated H3 (the IP value was normalized to the input). (c) U2OS cells were expressed with the indicated H3 proteins. ChIP analyses with an anti-Ku70 antibody were performed at the indicated time points after I-SceI transfection. Immunoblotting analyses were performed with the indicated antibodies. (d) GSC11 cells were expressed with a vector for control shRNA, FH shRNA (left panel), H2A.Z shRNA (right panel) and were reconstituted with the indicated FH or H2A.Z protein expression. Immunoblotting analyses were performed with the indicated antibodies. (e) U2OS cells were expressed with a vector for control shRNA or KDM2B shRNA. Immunoblotting analyses were performed with the indicated antibodies. (f) U2OS cells with depleted FH and reconstituted expression of the indicated FH proteins or with depleted H2A.Z and reconstituted expression of the indicated H2A.Z proteins were transfected with a vector expressing I-SceI. ChIP analyses with an anti-KDM2B antibody were performed 30 h after I-SceI transfection. # stands for no statistical significance between the indicated samples and the WT counterparts. (g) GSC11 cells with depleted endogenous KDM2B were exposed to IR (10 Gy) and harvested 1 h after IR. Chromatin extracts were incubated with malate (2.5 mM) in the presence or absence of αKG (50 μM or 2.5 mM) for 30 min, followed by incubation with KDM2B.

Supplementary Figure 7 Fumarate produced by chromatin-associated FH promotes cell survival.

(ae) Data represent one out of 3 experiments unless specifically indicated. (a) The indicated cells were expressed with a vector for control shRNA or FH shRNA and reconstituted with the indicated FH proteins. Immunoblotting analyses were performed with the indicated antibodies. (b) The indicated cells were expressed with a vector for control shRNA or H2A.Z shRNA and reconstituted with the indicated H2A.Z proteins. Immunoblotting analyses were performed with the indicated antibodies. (c,d) Thymidine double block-synchronized HeLa and A549 cells with depleted endogenous FH and reconstituted expression of the indicated FH proteins (c) or with depleted endogenous H2A.Z and reconstituted expression of the indicated H2A.Z proteins (d) were exposed to IR (10 Gy) and harvested after 1 h. Chromatin extracts were prepared. Immunoblotting analyses were performed with the indicated antibodies. (e) The indicated cells were expressed with a vector for control shRNA or KDM2B shRNA. Immunoblotting analyses were performed with the indicated antibodies. (f,g) The indicated synchronized cells with depleted endogenous FH and reconstituted expression of the indicated FH proteins (f) or with depleted endogenous H2A.Z and reconstituted expression of the indicated H2A.Z proteins (g) were transfected with or without a vector expressing KDM2B shRNA and exposed to IR (10 Gy). Cell viability was measured 12 h after IR by using the trypan blue assay. The data represent the mean ± SD (n = 3 independent experiments).

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Jiang, Y., Qian, X., Shen, J. et al. Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation. Nat Cell Biol 17, 1158–1168 (2015). https://doi.org/10.1038/ncb3209

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