Research ArticleCELL BIOLOGY

NuRD mediates mitochondrial stress–induced longevity via chromatin remodeling in response to acetyl-CoA level

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Science Advances  31 Jul 2020:
Vol. 6, no. 31, eabb2529
DOI: 10.1126/sciadv.abb2529
  • Fig. 1 Identification and characterization of DVE-1–associated NuRD complex in UPRmt signaling.

    (A) List of DVE-1–interacting proteins that belong to the NuRD complex identified by IP-MS experiments. Dve-1p::dve-1::gfp transgenic worms grown on empty vector (EV) and cco-1 RNAi bacteria were used for anti-GFP IP and MS. All proteins that belong to the NuRD complex were detected multiple times in three biological replicates. Score reflects the combined scores of all observed mass spectra that can be matched to amino acid sequences within a protein. A higher score indicates a more confident match. (B) Simplified model of NuRD complex subunits in C. elegans. (C) Validation of the interaction between DVE-1 and the NuRD complex. Lin-40p::lin-40::Flag::mCherry transgenic animals grown on EV or cco-1 RNAi bacteria were used for in vivo IP experiments followed by Western blot analyses using anti–DVE-1 antibody. Wild-type (WT) animals were used as negative control. (D) Representative photomicrographs of dve-1p::dve-1::gfp reporter in day-1 adult animals grown on EV, cco-1 + EV, cco-1 + lin-40, cco-1 + lin-53, cco-1 + dcp-66, cco-1 + let-418, or cco-1 + hda-1 double-RNAi bacteria from hatch. The posterior region of the intestine where DVE-1::GFP is induced or suppressed is highlighted with a white line. Scale bar, 250 μm. (E) Quantification of the number of intestinal nuclei with GFP signal per worm. The treatment is as shown in (D). ***P < 0.0001 via t test. Error bars, SEM; n ≥ 15 worms. (F) Representative photomicrographs of dve-1::gfp animals grown on EV, cco-1 + EV, or cco-1 + lin-40 double-RNAi bacteria from hatch. Dash rectangles highlight the areas enlarged and shown on the right. Scale bars, 25 μm.

  • Fig. 2 NuRD complex subunits accumulate in the nucleus in response to mitochondrial stress.

    (A) Representative photomicrographs of LIN-40::mCherry animals in a WT or atfs-1 mutant background grown on EV, cco-1 + EV, or cco-1 + dve-1 double-RNAi bacteria from hatch. Scale bar, 25 μm. (B) Quantification of the number of intestinal nuclei with strong mCherry signal in animals as shown in (A). (C) Representative photomicrographs of lin-53p::lin-53::gfp animals in a WT or atfs-1 mutant background grown on EV, cco-1 + EV, or cco-1 + dve-1 double-RNAi bacteria from hatch. Scale bar, 25 μm. (D) Quantification of the number of intestinal nuclei with strong GFP signal in animals as shown in (C). ***P < 0.0001, ns denotes P > 0.05 via t test. Error bars, SEM; n ≥ 15 worms.

  • Fig. 3 The NuRD complex is required for the mitochondrial stress–induced global chromatin reorganization.

    (A) Representative maximal intensity projection images of 4′,6-diamidino-2-phenylindole (DAPI) immunostaining of intestinal nuclei in day-1 adult WT, lin-40, or lin-53 mutant animals grown on EV, cco-1 + EV, EV + hda-1, cco-1 + hda-1, EV + dcp-66, or cco-1 + dcp-66 double-RNAi bacteria from hatch. The red arrow indicates the intestinal nucleus; the area circled by a yellow dotted line or asterisk denotes nucleus of other tissues (e.g., germ cell and muscle). DAPI (grey); Scale bar, 25 μm. (B) Quantification of the intestinal nuclear maximum cross-section area at day 1 of adulthood in animals as shown in (A). n ≥ 25 nuclei. (C) Immunoblots of histone H3Ac, H3K9Ac, H3K14Ac, and H3K27Ac in WT or lin-40 animals grown on EV or cco-1 RNAi. Anti-histone H3 serves as loading control. (D) Quantified mean data of histone H3Ac, H3K9Ac, H3K14Ac, and H3K27Ac levels (relative to histone H3). n = 3. (E) Representative maximal intensity projection images of DAPI immunostaining of intestinal nuclei at day 1 of adulthood in animals grown on EV or cco-1 RNAi from hatch with or without sodium butyrate treatment. DAPI (grey); Scale bar, 25 μm. (F) Quantification of the intestinal nuclear maximum cross-section area at day 1 of adulthood in animals, as shown in (E). n ≥ 25 nuclei. **P < 0.01 and ***P < 0.0001 and ns denotes P > 0.05 via t test. Error bars, SEM.

  • Fig. 4 Effects of acetyl-CoA abundance on chromatin structure and the NuRD complex in response to mitochondrial stress.

    (A) Illustration diagram showing that acetyl-CoA availability is nutrient dependent and dynamically regulates histone acetylation levels. Presence of pyruvate, citrate, and acetate contributes to the production of acetyl-CoA for histone acetylation. (B) Citrate concentration measurement of L4 worms grown on EV or cco-1 RNAi bacteria using whole-worm lysate. n = 3. (C) Acetyl-CoA concentration measurement of L4 worms grown on EV or cco-1 RNAi bacteria using whole-worm lysate. n = 3. (D) Representative maximal intensity projection images of DAPI immunostaining of intestinal nuclei in day-1 adult animals grown on EV or cco-1 RNAi bacteria with or without citrate (50 mM), acetate (10 mM), pyruvate (10 mM), or glucose (10 mM) treatment. DAPI (grey). The red arrow indicates the intestinal nucleus. Scale bar, 25 μm. (E) Quantification of the intestinal nuclear maximum cross-section area at day 1 of adulthood in animals as shown in (D). n ≥ 25 nuclei. (F) Representative photomicrographs of lin-40p::lin-40::Flag::mCherry animals grown on EV or cco-1 RNAi bacteria with or without different compounds treatment (as indicated). Pictures were taken at day 1 of adulthood. Scale bar, 25 μm. (G) Representative photomicrographs of dve-1p::dve-1::gfp animals grown on EV or cco-1 RNAi bacteria with or without different compounds treatment (as indicated). Pictures were taken at day 1 of adulthood. The posterior region of the intestine where DVE-1::GFP is induced or suppressed is highlighted with a white line. Scale bar, 250 μm. **P < 0.01 and ***P < 0.0001 via t test. Error bars, SEM.

  • Fig. 5 Reduction of acetyl-CoA synthesis causes chromatin structure changes mimicking mitochondrial stress.

    (A) Representative maximal intensity projection images of DAPI immunostaining of intestinal nuclei in day-1 adult WT animals grown on EV, cco-1, acly-1, acs-19, pdha-1, or pdhb-1 RNAi bacteria from hatch. DAPI (grey). Scale bar, 50 μm. (B) Quantification of the intestinal nuclear maximum cross-section area at day 1 of adulthood in animals as shown in (A). n ≥ 30 nuclei. (C) Representative photomicrographs of dve-1p::dve-1::gfp animals grown on EV, cco-1, acly-1, acs-19, pdha-1, or pdhb-1 RNAi bacteria from hatch. The posterior region of the intestine where DVE-1::GFP is induced or suppressed is highlighted with a white line. Scale bar, 250 μm. (D) Quantification of the number of intestinal nuclei with GFP signal in animals, as shown in (C). n = 15 worms. (E) Representative photomicrographs of lin-40p::lin-40::Flag::mCherry animals grown on EV, cco-1, acly-1, acs-19, or pdha-1 RNAi bacteria from hatch. Scale bar, 25 μm. (F) Quantification of the number of intestinal nuclei with strong mCherry signal in animals, as shown in (E). n ≥ 10 worms. (G) Representative photomicrographs of hsp-6p::gfp animals grown on EV, cco-1, acly-1, acs-19, pdha-1, or pdhb-1 RNAi bacteria from hatch. Scale bar, 250 μm. (H) Quantification of hsp-6p::gfp expression level of the entire intestine in animals, as shown in (G). n = 15 worms. ***P < 0.0001 and ns denotes P > 0.05 via t test. Error bars, SEM. a.u., arbitrary units.

  • Fig. 6 Dietary nutrients diminish mitochondrial stress–induced longevity.

    (A) Survival analyses of WT, lin-40(yth27), and lin-53(n833) animals on EV or cco-1 RNAi bacteria. (B) Representative photomicrographs of ges-1p::tomm-20::HA::mKate2 and myo-3p::tomm-20::HA::mKate2 animals in a WT or lin-40 mutant background grown on EV or cco-1 RNAi bacteria from hatch. Pictures were taken at day 1 of adulthood. Scale bar, 25 μm. (C) Survival analyses of WT and LIN-40 overexpression animals on OP50 bacteria. (D) Survival analyses of WT animals on EV or cco-1 RNAi bacteria with or without citrate (50 mM) or acetate (10 mM) treatment. (E) Survival analyses of WT animals on EV or cco-1 RNAi bacteria with or without pyruvate (10 mM) or glucose (10 mM) treatment. (F) Model of acetyl-CoA links mitochondrial stress to longevity via NuRD-mediated chromatin remodeling. Under nonstressed conditions, acetyl-CoA can be generated from citrate and acts as the substrate for histone acetylation. Under these conditions, DVE-1 and the NuRD complex do not accumulate in the nucleus, animals have normal life span, and nucleus is not compacted. During mitochondrial stress, decreased citrate level results in limited production of acetyl-CoA, leading to the accumulation of DVE-1 and NuRD in the nucleus. Consequently, the histone acetylation level is decreased, nuclei become compacted, and animals are long-lived.

Supplementary Materials

  • Supplementary Materials

    NuRD mediates mitochondrial stress–induced longevity via chromatin remodeling in response to acetyl-CoA level

    Di Zhu, Xueying Wu, Jun Zhou, Xinyu Li, Xiahe Huang, Jiasheng Li, Junbo Wu, Qian Bian, Yingchun Wang, Ye Tian

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