SIRT7 regulates dosage compensation and safeguards the female X chromosome

Abstract Sirtuins are deacetylases implicated in stress responses and longevity in mammals1,2. Although their differential impact on disease for the two sexes has been noted3,4,5,6,7, the underlying reasons are unclear. Here, using Sirt7 as a model in mice, we examine the mechanisms leading to sex differences and find that Sirt7−/− female mice have decreased fitness throughout their lifespan. Notably, SIRT7 preferentially localizes to the sex chromosomes. In female individuals, SIRT7 loss affects X-chromosome inactivation, the first arm of dosage compensation that equalizes X-linked gene expression between males and females8,9,10. Xist is overexpressed and gene silencing becomes more efficient. However, SIRT7 loss has greatest impact on the active X (Xa) chromosome. The Xa chromosome becomes hyperacetylated at Lys36 of histone H3, structurally disorganized, prone to DNA damage and overexpressed. Increased Xa-chromosome expression leads to genome imbalance and augmented X-chromosome upregulation—the second arm of dosage compensation that balances X-chromosome versus autosomal gene expression. These data reveal an essential crosstalk between sirtuins and the sex chromosomes, with SIRT7 safeguarding X-chromosome integrity and dosage balance with autosomes. We propose that the sex bias in SIRT7 biology can be explained in part by unequal effects on the sex chromosomes. This is a preview of subscription content, access via your institution Access options Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access subscription £17.99 / 30 days cancel any time Subscribe to this journal Receive 52 print issues and online access £199.00 per year only £3.83 per issue Buy this article - Purchase on SpringerLink - Instant access to the full article PDF. £ 29.95 Prices may be subject to local taxes which are calculated during checkout Data availability All new datasets generated from this work have been deposited in GEO under accession GSE256287. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository under dataset identifier PXD057198. Source data are provided with this paper. Code availability The custom code for RNA-seq and related ChIP–seq presented in this study is archived at Zenodo96 (https://doi.org/10.5281/zenodo.19464181). References Vaquero, A. 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Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983). Simonet, N. G. Code for ‘SIRT7 regulates dosage compensation and safeguards the female X-chromosome’. Zenodo https://doi.org/10.5281/zenodo.19464181 (2026). Acknowledgements We thank C. Wei for sharing So-Smart-seq data from pre-implantation embryos. We acknowledge the Office of Advanced Research Computing (OARC) at Rutgers, The State University of New Jersey, for providing access to the Amarel cluster and associated research computing resources that have contributed to the results reported here (https://oarc.rutgers.edu). Funding J.T.L. received funding from the US National Institutes of Health grants, R01-GM58839 and R01-HD097665. A.V. and A.R.-H. received funding from the Spanish Ministry of Science and Innovation (MICINN) grants PID2020-117284RB-I00 (A.V), PID2023-148760OB-I00 (A.V.) and PID2020–112557GB-I00 (A.R.-H.), supported by MCIN/AEI/10.13039/501100011033 and FEDER, and the Catalan Government Agency grant AGAUR 2021-SGR-01378 (A.V.) and 2021 SGR 122 (A.R.-H.). L.M.-G. was supported by the Ministry of Science, Innovation and University (FPU18/03867). Author information Authors and Affiliations Contributions N.G.S., A.V. and J.T.L. conceived the study, designed the experiments and wrote the paper. N.G.S. analysed data and performed ChIP–seq, RNA-seq, Xist RNA-FISH, EZH2-RIP, caspase 3/7 assays, X-ray treatments, CRISPR–Cas9 gene editing, RT–qPCRs and western blotting experiments. J.K.T. performed a majority of bioinformatics analyses. B.K. performed RNA-seq, scatterplot and vector analyses. A.L. performed high-resolution chromosome modelling and 3D organization. U.W. performed Xist CHART experiments. D.W. performed allelic-specific Hi-C alignment. F.S. performed bioinformatic analysis of Hi-C data. A.G.-S. established primary MEF lines and conducted fetal oocyte and spermatocyte chromosome spread analyses and mouse experimental procedures. M.E.-A. performed ChIP–seq, western blotting and RT–qPCR experiments. L.S. and B.N.V. provided mouse survival experiments and embryo analysis. J.C.-G. performed cloning and western blotting experiments. M.B. generated TsixTST/+Hprt-GFP Xi/+ reporter mES cell line. B.P. provided cell lines and expertise. A.R.-H. supervised L.M.-G. and C.M.-G. in carrying out metaphase spread experiments for immunofluorescence and DNA FISH. J.T. provided resources for the genetic analysis of mouse studies. L.R. generated Hi-C libraries. B.M.J. supervised F.S. and L.R. Corresponding authors Ethics declarations Competing interests J.T.L. is a non-executive director of GlaxoSmithKline and a cofounder of Fulcrum Therapeutics, and serves on the scientific advisory board of Skyhawk Therapeutics. The other authors declare no competing interests. Peer review Peer review information Nature thanks Björn Reinius and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Additional information Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Extended data figures and tables Extended Data Fig. 1 SIRT7 enrichment profiles on autosomes and ChrX. a, Metagene analysis showing average SIRT7 binding to X- and Y-linked genes versus autosomal genes in male E14.5 MEF. Mean ± 95% CI. b, Metagene profiles around the TSS (left panel) and TTS (right panel) for X-, Y- linked and autosomal genes in male MEF. Mean ± 95% CI. c, Scatterplot of SIRT7 densities on the mus and cas chromosomes of ChrX and Chr13 in TTF. SIRT7 ChIP signals normalized by input in 1MB non-overlapping bins. Red line, linear regression with 95% confidence interval. d, CEAS analysis showing the SIRT7-ChIP average gene profile on ChrX in TTF for mus (Xi) and cas (Xa) alleles. Mean ± 95% CI. e, Metagene profiles around the TSS (left panel) and TTS (right panel) for X-linked and autosomal genes in male and female TTF. Data are consistent with MEF data. Mean ± 95% CI. f, Scatterplot of SIRT7 densities on the mus and cas chromosomes of ChrX and Chr13 in non-clonal primary hybrid MEF with random XCI. n = 2 biologically independent cells, shown separately in left and right panels. SIRT7 ChIP signals normalized by input in 1MB non-overlapping bins. Red line, linear regression with 95% confidence interval. g, Western blot of SIRT7 in knockout and WT TTF cells. Tubulin, loading control. Positive control SIRT7-Flag: TTF cells ectopically overexpressing SIRT7-Flag. Blots are representative of three independent experiments with similar results. h, allele-specific SIRT7 ChIP-seq IGV tracks in WT and Sirt7−/− TTF across the X-chromosome (top) and chromosome 13 (bottom) for mus (Xi:) and cas (Xa:). Extended Data Fig. 2 Dysregulation of Xa and Xi expression. a, Expression levels of indicated genes based on RNA-seq data from differentiating female mESC from days 5 to 14. FPKM values were calculated from a single replicate for each time point using data from GSE135389. b, Western blot of SIRT7 with H3 loading control for WT mESC. c, Quantification of SIRT7 protein levels across mESC differentiation days 0–7 using Western blot analysis. The centre represents the mean, and error bars ±SEM. n = 3 biologically independent cells. One-way ANOVA. d, Western blot of SIRT7 and H3K36ac, with H3 loading control for WT and Sirt7−/− female mESC clones. e, Nanog, Oct4, and Sirt7 RT-qPCRs of differentiating WT and Sirt7−/− mESC at days 0, 3, 7. WT day 0 used as control reference (value 1.0). All levels normalized to GAPDH. Mean ± SEM are shown. n = 4 biologically independent cells. P-values; Tukey’s multiple comparisons test. f, SIRT7-deficient mESC form EBs. Micrographs are representative of three independent experiments with similar results. Scale bars, 150 μm g, Bar plot of significantly up- and down-regulated in Sirt7−/− relative to WT mESC at day 7. Xa and Xi genes shown separately. h, Venn diagram of significantly up- and down-regulated genes in Sirt7−/− relative to WT mESC at day 7. i, TsixTST/+; Hprt-GFP Xi/+ reporter mESC line at days 0, 3, and 7 of differentiation. Bright-field and GFP fluorescence channels are shown. Scale bars, 150 μm. j, GFP and Xist expression levels across 7 days of mESC differentiation. Sirt7−/− cells are of TsixTST/+; Hprt-GFP Xi/+ background. Values are normalized to GAPDH and expressed relative to day 0. The center represents the mean, and error bars indicate ±SD from n = 3 biologically independent cells. Statistical significance between WT and Sirt7−/− at each time point was determined using two-sided multiple ratio-paired t-tests. P-values shown were adjusted for multiple comparisons using the Holm-Šídák method. ns, not significant. k, Measurement of the XCI efficiency using the area under the curve (AUC) metric: (AUC_XistSirt7−/−/AUC_XistWT)÷(AUC_GFPSirt7−/−/ AUC_eGFPWT). AUC values were derived from quadratic (second-order polynomial) interpolation of Xist and GFP expression trajectories from days 0 to 7 of differentiation. Sirt7−/− cells are of TsixTST/+; Hprt-GFP Xi/+ background. l, Scatterplots correlating log2 FPKM values of escapee genes in Sirt7−/− versus WT day 7 mESC. Xa and Xi plotted separately. Linear regression: Dotted line x = y, expected. Solid line, observed. Slope, two-sided P-value (binomial test for mutant overexpression relative to WT), intercept, and R² for the linear regression are shown. Extended Data Fig. 3 Direct correlation between H3K36ac changes and changes in POL-II transcription. a-c, Pie charts depicting the location of H3K36ac ChIP-seq peaks relative to gene locations on Xa, Xi, and autosomes in WT and Sirt7−/−. d, Heatmap (upper panels) and corresponding metagene analysis (lower panels) of H3K36 levels in relation to POL-II peaks (x = 0). H3K36ac ChIP-seq signals are plotted ±3 kb from the center of POL-II peaks. Xa and Xi profiles shown separately for WT and Sirt7−/− in mESC at day 7. e, Heatmap (upper panels) and corresponding metagene analysis (lower panels) of H3K36 levels in relation to POL-II peaks (x = 0). H3K36ac ChIP-seq signals are plotted ±3 kb from the center of POL-II peaks. Comp reads (non-allelic) are shown for WT and Sirt7−/− in mESC at day 7. f, Synergy vector analysis to examine directionality of change for H3K36ac enrichment relative to gene expression changes in Sirt7−/− relative to WT mESCs at day 7. RNA-seq and ChIP-seq (H3K36ac) values were Log2-transformed (value + 1). Vectors are filtered for an absolute angle > 10°. Vector colours reflect Benjamini–Hochberg corrected FDR values. g, Violin plots showing distribution density of synergy scores for the up- and down-DEGs in panel f. Sirt7−/− vs. WT mESCs at day 7 after LIF withdrawal, calculated separately for Up- and Down-DEGs. The synergy score reflects the extent to which H3K36ac and RNA expression changes occur together. High values indicate strong coordinated increases or decreases, whereas and low or negative values weak or opposing responses. Embedded box plots indicate the median (centre line), the first and third quartiles (box bounds), and whiskers extending to the absolute minima and maxima. n = 3 biologically independent cells. P-value; two-sided Wilcoxon test. Extended Data Fig. 4 Gene ontology phenotypes associated with SIRT7. a, GO analysis displaying the Mouse Phenotype Single KO terms of H3K36ac peaks on Xa and autosomes in Sirt7−/− using GREAT. Phenotype enrichments are ranked by -Log10 of the one-sided binomial test P-value. b, GO analysis displaying Mouse Phenotype terms of H3K36ac peaks on Xi and autosomes in Sirt7−/− using GREAT. Phenotype enrichments are ranked by -Log10 of the one-sided binomial test P-value. c, GO analysis displaying the Mouse Phenotype terms of H3K36ac peaks on Xa in Sirt7−/− using GREAT. Phenotype enrichments are ranked by -Log10 of the one-sided binomial test P-value. d, GO analysis displaying Human Phenotype KO terms of H3K36ac peaks on Xa and autosomes in Sirt7−/− using GREAT. Phenotype enrichments are ranked by -Log10 of the one-sided binomial test P-value. Extended Data Fig. 5 Increased Xist expression and H3K27me3 enrichment on the Xi. a, RT-qPCR of Xist expression in WT and Sirt7−/− MEF and TTF, normalized to GAPDH. Mean +/- SE from n = 3 biologically independent replicates (MEF) and n = 5 biologically independent replicates (TTF). *P = 0.0341, **P = 0.0077, Two-sided Student’s t-test. b, Xist RNA FISH in WT and Sirt7−/− TTF. DAPI staining (blue). Scale bars, 10 μm. c, Quantitation of Xist signals from the FISH experiment of c. Xist integrated density for WT and Sirt7−/− TTF. Horizontal line represents the mean value, and the error bars ±SD. n = 2 biologically independent replicates. ****P ≤ 0.0001, Two-sided Student’s t-test. d, Xist CHART-seq (mus allele) and H3K36ac ChIP-seq tracks along the Xist locus in a 22 kb window (tracks from IGV) in TTF and mESC (day 7) in WT and SirT7−/−. Normalized read densities are displayed in mus, cas, and composite (comp). Extended Data Fig. 6 3D structural changes on the Xa and Xi. a, Hi-C contact heatmaps of for the Xi and Xa in WT and Sirt7−/− TTF binned at 250-kb resolution. Grey-shaded areas, unmappable regions. b, Scatterplot showing the correlation between differences in H3K27me3 signals (ChIPseq) and PC1 values (Hi-C) between Sirt7−/− vs. WT TTF. Linear regression line (red), Pearson’s correlation coefficient (R) shown. Significance (P-value, two-sided Pearson’s correlation test) of the difference between the slope of the regression line and slope=0 is shown. Red line, linear regression with 95% confidence interval. c, Scatterplot showing correlation of PC1 values for Xi genes in Sirt7−/− vs. WT TTF. Heatmap shows the gain of H3K27me3 signals for each gene in the scatterplot. Red box, 37 Xi DEGs that switched to a positive PC1 (per Fig. 4a, boxed regions). d, CDF plots of gene expression from 37 Xi DEGs in panel d. Notably, the DEGs are downregulated in Sirt7−/− relative to WT TTF. P-value; two-sided Wilcoxon test. e, Insulation scores at domain borders (x = 0) on Chr13 in WT and Sirt7−/−. P-value; two-sided Mann-Whitney test. f, Insulation scores at domain borders of the Xa, Xi, and Chr13 in WT and Sirt7−/−. Note: y-axis plots WT – Sirt7−/− (thus, a higher score means less insulation in the mutant). Box plots show the median (centre line), first and third quartiles (box bounds), and whiskers extending to the most extreme data points within 1.5 × IQR. Notches indicate the bootstrap-estimated 95% confidence interval around the median (1000 resamples). n = 2 biologically independent cells. P-value; two-sided Mann-Whitney test. g, Insulation score at topological domain borders on the Xa or Xi in WT and Sirt7−/−. P-value; two-sided Mann-Whitney test. h, Average of mixing coefficients between A and B compartments for the Xa or Xi in WT and Sirt7−/− cells. *P = 0.035, two-sided Student’s t-test. i, Quantitative analysis of PC1 variance, A-B mixing scores, local mixing index (note: lower score means higher mixing), boundary sharpness, and domain insulation scores for the Xa and Xi in Sirt7−/− TTF. j, Correlation between H3K36ac ChIP-seq and PC1 values on the Xa and Xi in WT and Sirt7−/−. Linear regression line (red), Pearson’s correlation coefficient (R) shown. Significance (P-value, two-sided Pearson’s correlation test) of the difference between the slope of the regression line and slope=0 is shown. Red line, linear regression with 95% confidence interval. k, 3D reconstruction using 4DHiC to visualize the A/B compartments in relation to H3K36ac on the Xa and Xi. Extended Data Fig. 7 SIRT7 safeguards the female X chromosome. a, Percentage (%) of metaphases showing fusion chromosomes in WT and Sirt7−/− female TTF. Sample size (n) shown. b, Percentage (%) of metaphases showing fusion chromosomes in WT and Sirt7−/− MEF of male or female origin. Pearson’s chi-squared test. ns, not significant. c, Percentage (%) of metaphases showing endoduplications in WT and Sirt7−/− female MEF. Normal karyotype, 2n = 40 chromosomes. Endoduplications, 2n = 80 chromosomes. Pearson’s chi-squared test. ns, not significant. d, Metaphase spreads analysis using an X-painting probe to detect chromosomal fusions between the X chromosome and autosomes in female WT and Sirt7−/− MEFs. Pearson’s chi-squared test. ns, not significant. e, Percentage (%) of metaphases showing indicated fusion chromosomes in WT and Sirt7−/− female mESC. Pearson’s chi-squared test. ns, not significant. f, Western blot of SIRT7, γH2AX, and H2AX from WT and Sirt7−/− primary MEF (male and female) after H2O2-treatment (1 mM) for 10 min. g, Quantification of DSB in female and male WT and Sirt7−/− MEF. γH2AX ChIP-seq normalized read counts (normalized to H2AX) in autosomes and ChrX from after 30 min of recovery following 5 Gy X-ray irradiation. Boxplots show quartiles with whiskers at 1.5 × IQR; outliers are shown individually. n = 2 biologically independent cells. P-values; two-sided Student’s t-test. Extended Data Fig. 8 SIRT7 deficiency is associated with DSB and asynapsis during female meiosis. a, Illustration of E14.5 female embryo and meiotic germ cells in the fetal ovary. Created in BioRender; Simonet Dominguez, N. https://BioRender.com/ao54ngo (2026). b, Immuno-DNA FISH of E17.5 pachytene stage oocytes from WT and Sirt7−/− female mouse embryos. X-painting probes mark ChrX. Immunostains of SYCP3 and HORMAD1 mark synapsed versus asynapsed regions, respectively. Representative images selected from 9 biologically independent embryos (WT, n = 5; Sirt7−/−, n = 4). This experiment was performed independently for each biological replicate with similar results. DNA, DAPI staining (blue). Scale bars, 10 μm. c, Immunostaining of pachynema spermatocytes from WT and Sirt7−/− male mice. γH2AX stain mark the XY body. SYCP3 mark synapsed autosomes. Scale bars, 10 μm. d, Quantification of γH2AX intensity in the XY body of WT and Sirt7−/− pachynema spermatocytes. The centre represents the mean, and error bars ±SD. Two-sided Student’s t-test. ns, not significant. Extended Data Fig. 9 SIRT7 regulates XCU. a, Expression of Sirt7, Nanog and Xist from single preimplantation mouse female embryos, as analysed from published RNAseq data10. CPKM, counts per kilobase per million. Mean ± SD. Sample sizes for each embryo state: n = 4 (late2C), n = 5 (4 C), n = 9 (8 C), n = 7 (16 C), and n = 5 (early blastocyst) b, Heatmap (top) and metagene profiles (bottom) of H3K36ac signals on the future-Xi, future-Xa, and Chr13-cas in day 0 mESC. TSS to TTS ± 5 kb is plotted. c, Heatmap (top) and metagene profiles (bottom) of composite (comp) H3K36ac signals for ChrX, Chr13, and all autosomes in day 0 WT versus Sirt7−/− mESC. d, Heatmap (top) and metagene profiles (bottom) of composite (comp) H3K36ac signals for ChrX, Chr13, and all autosomes in day 7 WT versus Sirt7−/− mESC. e, Metagene plot of fold-change in H3K36ac signals on the Xi versus Chr13-mus in day 0 and day 7 WT versus Sirt7−/− mESC. Significance (P-value; two-sided KS test) of the difference over the first quarter of the metagene body is shown. f, CDF plots of Log2FC in Sirt7−/− vs WT MEF for X-linked and Chr13 genes. Female and male MEFs shown in separate plots with FPKM cutoff of >=0.5. P, determined by a two-sided KS test. g, MA Bland–Altman plot showing Log2 fold-change of Sirt7−/− vs. WT male MEF and average log2 counts per million (cpm) of mapped reads for each Y-linked gene. Differential expression was assessed using edgeR quasi-likelihood negative binomial generalized linear models (FPKM cutoff ≥ 0.5). Statistical significance was determined via quasi-likelihood F-test with P-values adjusted for multiple testing using the Benjamini-Hochberg false discovery rate procedure. ns, non-significant. Extended Data Fig. 10 SIRT7 rescue experiment. a, Amino acid substitution of SIRT7 (H187Y) generated by CRISPR/Cas9–mediated homology-directed repair (HDR) in TTF cells, confirmed by Sanger sequencing. b, Western blot of SIRT7, H3K36ac, and H3 in WT, Sirt7−/−, and three independent clones obtained by CRISPR knock-in Sirt7H187Y in TTF cells. Blots are representative of two independent experiments with similar results. Supplementary information Supplementary Information (download PDF ) Supplementary Figs. 1 and 2, the legends for Supplementary Videos 1–4 and the legends for Supplementary Tables 1–17. Supplementary Tables (download ZIP ) Supplementary Tables 1–17. Supplementary Video 1 (download MP4 ) 3D Hi-C models of Xa A/B compartments in WT (left) and Sirt7−/− (right) TTF, with A compartments in red and B compartments in blue. Supplementary Video 2 (download MP4 ) 3D Hi-C models of Xa H3K36ac enrichment in WT (left) and Sirt7−/− (right) TTF. White indicates no enrichment, and increasing H3K36ac enrichment is shown from light to dark green. Supplementary Video 3 (download MP4 ) 3D Hi-C models of Xi A/B compartments in WT (left) and Sirt7−/− (right) TTF, with A compartments in red and B compartments in blue Supplementary Video 4 (download MP4 ) 3D Hi-C models of Xi H3K36ac enrichment in WT (left) and Sirt7−/− (right) TTF. White indicates no enrichment, and increasing H3K36ac enrichment is shown from light to dark green Rights and permissions Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. About this article Cite this article Simonet, N.G., Thackray, J.K., Kesner, B. et al. SIRT7 regulates dosage compensation and safeguards the female X chromosome. Nature (2026). https://doi.org/10.1038/s41586-026-10645-x Received: Accepted: Published: Version of record: DOI: https://doi.org/10.1038/s41586-026-10645-x