SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging

Abstract

Genomic instability and alterations in gene expression are hallmarks of eukaryotic aging. The yeast histone deacetylase Sir2 silences transcription and stabilizes repetitive DNA, but during aging or in response to a DNA break, the Sir complex relocalizes to sites of genomic instability, resulting in the desilencing of genes that cause sterility, a characteristic of yeast aging. Using embryonic stem cells, we show that mammalian Sir2, SIRT1, represses repetitive DNA and a functionally diverse set of genes across the mouse genome. In response to DNA damage, SIRT1 dissociates from these loci and relocalizes to DNA breaks to promote repair, resulting in transcriptional changes that parallel those in the aging mouse brain. Increased SIRT1 expression promotes survival in a mouse model of genomic instability and suppresses age-dependent transcriptional changes. Thus, DNA damage-induced redistribution of SIRT1 and other chromatin-modifying proteins may be a conserved mechanism of aging in eukaryotes.

Figure 1

Oxidative stress reduces Sir2/SIRT1-mediated repetitive DNA silencing in yeast and mammalian cells. (A–C). Effects of H₂O₂ on yeast aging. (A) H₂O₂ causes loss of silencing at the mating type loci. Shown is the fraction of GFP⁺ cells in 2xSIR2 and WT cells. Unless otherwise noted, P values are based on Student’s two-tailed t test with #P≤ 0.1, *P≤ 0.05, **P≤ 0.01, ***P≤ 0.001. (B) Frequency of H₂O₂-induced rDNA recombination in the absence presence of extra Sir2 (WT and Sir2 o/e). (C) Replicative lifespan of WT and 2xSIR2 cells grown in the absence or presence of 1 mM H₂O₂. (D) Mouse SIRT1 binds to repetitive genomic DNA. ChIP for SIRT1 or control immunoglobulin (Ig) at major satellite repeats in the absence or presence of NAM (25 mM) (E) q-PCR analysis of ChIP experiments using antibodies specific for SIRT1 or H1AcK26. ES cells were left untreated or treated with H₂O₂ (2 mM) or NAM for 1 h. (F) Oxidative stress increases transcription of satellite repeat DNA. ES cells were treated with NAM for 24 h or with H₂O₂ for 1 h, followed by 23 h recovery. (G) Cells with a targeted extra copy of SIRT1 and control cells were treated with H₂O₂ and analyzed as in (F). The inset shows a Western blot of SIRT1 in WT (black) and SIRT1 overexpressing ES cells (white). Data are represented as mean +/− SEM.

Figure 2

Oxidative stress causes a major redistribution of SIRT1. (A) Distribution of SIRT1 and H1AcK26 along a representative chromosome. ES cells were either untreated or treated with H₂O₂ for 1 h, followed by ChIP for SIRT1, H1AcK26 or control Ig. The x-axis depicts probe sets spanning the promoters of annotated ORFs, signals across the y-axis reflect the log₂ change of IP DNA over input DNA. (B) Significance of overrepresentation of selected gene ontology (GO) groups amongst SIRT1-associated genes before and after H₂O₂ treatment. Asterisks indicate significance after Benjamini- Hochberg false discovery rate correction. (C) Loss of SIRT1 binding correlates with increased H1K26 acetylation. Promoters with ≥ 2log₂ enrichment of SIRT1 prior to H₂O₂ treatment, but no signal thereafter were compared to non-SIRT1 associated promoters. The y-axis shows the fraction of promoters with a ≥ 2-fold increase in H1AcK26 enrichment after exposure to H₂O₂. SIRT1 and H1AcK26 probe set binding is shown for four of these promoters. GAPDH served as a negative control.

Figure 3

Transcriptional deregulation of SIRT1-associated genes in response to oxidative stress is repressed by increasing SIRT1 levels. (A) SIRT1 expression in wild-type (WT) and SIRT1 overexpressing (OE) ES cells. (B) q-RT-PCR analysis of putative SIRT1 target genes (SIRT1-bound), non-SIRT1-bound control genes and β-actin in wild-type (open bars) and SIRT1 overexpressing ES cells (closed bars). Shown is the fold change of expression compared to untreated samples. Data are represented as mean +/− SEM.

Figure 4

SIRT1 is recruited to chromatin upon DNA damage in an ATM-dependent manner. (A) Western blot analysis of SIRT1 and indicated control proteins in both chromatin-bound and non-chromatin-bound protein fractions from ES cells that were either left untreated or treated with H₂O₂ or MMS for 1 h. (B and C) Western blot analysis of chromatin-bound SIRT1 in response to H₂O₂ with or without pretreatment with wortmannin or KU55933 (B), and in the presence or absence of H2AX (C). (D and E) Recruitment of SIRT1 and Rad51 to chromatin in WT or SIRT1-deficient (SIRT1-Δex4) cells in response to H₂O₂ or IR.

Figure 5

SIRT1 is recruited to DNA breaks and is required for efficient DSB repair. (A) SIRT1 expression in parental U2OS-DRGFP cells, three independent shSIRT1 expressing cell lines (SIRT1-KD) and shRFP expressing controls. (B) ChIP analysis of SIRT1 and Nbs1 binding to a DSB in shRFP (control) and SIRT1 KD cells from (A). (C) DSB ChIP analysis of Rad51 recruitment using Ds-red-transfected (−) or I-SceI transfected cells (+) from (B) 24h after transfection. (D) SIRT1 knock-down results in reduced DSB repair as measured by GFP rexpression (see Figure S7A). Control and SIRT1-KD cell lines from (A) were transfected as in (C) and analyzed by FACS. (E) Loss of SIRT1 causes increased genomic instability upon oxidative stress. Untreated or H₂O₂ treated shSIRT1- or control shRNA-expressing ES cells were subjected to Q-FISH analysis. Telomeres are shown in red. Arrows indicate a chromatid break (left) and a fused centromere (right). The fraction of aberrant metaphases is shown. Data are represented as mean +/− SEM.

Figure 6

Increased SIRT1 activity alters tumor spectrum and increases survival of irradiated p53^+/− mice. (A) Survival of irradiated p53^+/− mice fed normal or resveratrol-supplemented chow (n=19 and 25, respectively). Tumor-related deaths were recorded in days after irradiation. (B) Tumor spectrum from mice in (A), legend lists dominant tumor at time of death; ^#no tumors detected in necropsy. (C) Western blot analysis of MACS-purified thymic CD4/CD8 double-positive (DP) T cells and splenic CD8⁺ T cells from MISTO mice (+ Mx-cre) and littermate controls (− Mx-cre). Mice were analyzed 14 days after Mx-cre induction; Thy: Thymus, Spl: Spleen. (D) SIRT1 mRNA expression in lymphocyte subsets from MISTO mice (closed bars) and littermate controls (open bars). BM: Bone marrow, Lin⁺: Lineage-positive. (E) Survival of MISTO and control p53^+/− mice (n=12 and 16, respectively) in response to a single dose of 4 Gy γ-irradiation. Tumor-related deaths were recorded in days after irradiation. (F) Tumor spectrum in mice from (E), legend as in (B).

Figure 7

Transcriptional deregulation of SIRT1 target genes occurs during normal aging. (A) Expression of SIRT1-associated gene from Figure 3 in the neocortex from young (5 months) and old (30 months) B6C3F₁ mice (n ≥ 6 per group), analyzed by q-PCR. Shown is the fold change in expression in old relative to young mice. P values are based on student’s one-tailed t-test. (B) Microarray expression analysis of SIRT1 target genes in the neocortex of young and old B6C3F₁ mice (n = 5 per group). SIRT1 target genes are significantly overrepresented amongst age-upregulated genes (χ² = 7.28, P = 0.0055). (C) Immunofluorescence analysis of SIRT1 and NeuN expression in the neocortex of NeSTO mice and Nestin-cre littermate controls. (D) q-RT-PCR analysis of SIRT1-bound genes from (A) and non-SIRT1-bound genes including housekeeping genes (rps16, hprt) and genes upregulated in 30 months old mice by microarray. NeSTO mice and Nestin-cre littermate controls (Control) were analyzed at 8–10 months (young, n = 3–5 and 6, respectively) or 18–19 months of age (old, n = 4 and 5, respectively). P values are based on student’s one-tailed t-test. Data are represented as mean +/− SEM.