Histone variants are structural components of eukaryotic chromatin that can replace replication-coupled histones in the nucleosome. The histone variant macroH2A1.1 contains a macrodomain capable of binding NAD+-derived metabolites. Here we report that macroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and that myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity. We found that the metabolite-binding macrodomain was essential for sustained optimal mitochondrial function but dispensable for gene regulation. Through direct binding, macroH2A1.1 inhibits basal poly-ADP ribose polymerase 1 (PARP-1) activity and thus reduces nuclear NAD+ consumption. The resultant accumulation of the NAD+ precursor NMN allows for maintenance of mitochondrial NAD+ pools that are critical for respiration. Our data indicate that macroH2A1.1-containing chromatin regulates mitochondrial respiration by limiting nuclear NAD+ consumption and establishing a buffer of NAD+ precursors in differentiated cells.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


Primary accessions

Gene Expression Omnibus


  1. 1.

    , & NAD+ metabolism in health and disease. Trends Biochem. Sci. 32, 12–19 (2007).

  2. 2.

    & The dynamic regulation of NAD metabolism in mitochondria. Trends Endocrinol. Metab. 23, 420–428 (2012).

  3. 3.

    & Poly(ADP-ribose) polymerase 1 at the crossroad of metabolic stress and inflammation in aging. Aging (Albany NY) 1, 458–469 (2009).

  4. 4.

    Biology of poly(ADP-ribose) polymerases: the factotums of cell maintenance. Mol. Cell 58, 947–958 (2015).

  5. 5.

    & New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs. Nat. Rev. Mol. Cell Biol. 13, 411–424 (2012).

  6. 6.

    , & NAD+ metabolism and the control of energy homeostasis: a balancing act between mitochondria and the nucleus. Cell Metab. 22, 31–53 (2015).

  7. 7.

    et al. MacroH2A histone variants maintain nuclear organization and heterochromatin architecture. J. Cell Sci. 130, 1570–1582 (2017).

  8. 8.

    & Approaching the molecular and physiological function of macroH2A variants. Epigenetics 5, 118–123 (2010).

  9. 9.

    , & Macro domains as metabolite sensors on chromatin. Cell. Mol. Life Sci. 70, 1509–1524 (2013).

  10. 10.

    , , , & The characterization of macroH2A beyond vertebrates supports an ancestral origin and conserved role for histone variants in chromatin. Epigenetics 11, 415–425 (2016).

  11. 11.

    et al. Structural characterization of the histone variant macroH2A. Mol. Cell. Biol. 25, 7616–7624 (2005).

  12. 12.

    , , , & Splicing regulates NAD metabolite binding to histone macroH2A. Nat. Struct. Mol. Biol. 12, 624–625 (2005).

  13. 13.

    et al. A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat. Struct. Mol. Biol. 16, 923–929 (2009).

  14. 14.

    et al. DNA repair factor APLF is a histone chaperone. Mol. Cell 41, 46–55 (2011).

  15. 15.

    & Loss of ATRX suppresses resolution of telomere cohesion to control recombination in ALT cancer cells. Cancer Cell 28, 357–369 (2015).

  16. 16.

    et al. A family of macrodomain proteins reverses cellular mono-ADP-ribosylation. Nat. Struct. Mol. Biol. 20, 508–514 (2013).

  17. 17.

    et al. Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat. Struct. Mol. Biol. 20, 502–507 (2013).

  18. 18.

    et al. The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat. Struct. Mol. Biol. 16, 1074–1079 (2009).

  19. 19.

    et al. The histone variant macroH2A suppresses melanoma progression through regulation of CDK8. Nature 468, 1105–1109 (2010).

  20. 20.

    , , & Histone variant macroH2A confers resistance to nuclear reprogramming. EMBO J. 30, 2373–2387 (2011).

  21. 21.

    et al. Developmental changes in histone macroH2A1-mediated gene regulation. Mol. Cell. Biol. 27, 2758–2764 (2007).

  22. 22.

    et al. Histone variant macroH2A1 deletion in mice causes female-specific steatosis. Epigenetics Chromatin 3, 8 (2010).

  23. 23.

    et al. Genetic ablation of macrohistone H2A1 leads to increased leanness, glucose tolerance and energy expenditure in mice fed a high-fat diet. Int. J. Obes. (Lond.) 39, 331–338 (2015).

  24. 24.

    , , & Mice without macroH2A histone variants. Mol. Cell. Biol. 34, 4523–4533 (2014).

  25. 25.

    et al. Histone macroH2A isoforms predict the risk of lung cancer recurrence. Oncogene 28, 3423–3428 (2009).

  26. 26.

    et al. The histone variant MacroH2A1.2 is necessary for the activation of muscle enhancers and recruitment of the transcription factor Pbx1. Cell Rep. 14, 1156–1168 (2016).

  27. 27.

    et al. Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497, 451–457 (2013).

  28. 28.

    , , & MacroH2A in stem cells: a story beyond gene repression. Epigenomics 4, 221–227 (2012).

  29. 29.

    et al. Pharmacological inhibition of poly(ADP-ribose) polymerases improves fitness and mitochondrial function in skeletal muscle. Cell Metab. 19, 1034–1041 (2014).

  30. 30.

    et al. PARP-1 inhibition increases mitochondrial metabolism through SIRT1 activation. Cell Metab. 13, 461–468 (2011).

  31. 31.

    et al. The histone variant mH2A1.1 interferes with transcription by down-regulating PARP-1 enzymatic activity. Genes Dev. 20, 3324–3336 (2006).

  32. 32.

    , , & Subcellular compartmentation and differential catalytic properties of the three human nicotinamide mononucleotide adenylyltransferase isoforms. J. Biol. Chem. 280, 36334–36341 (2005).

  33. 33.

    et al. MacroH2A1.1 and PARP-1 cooperate to regulate transcription by promoting CBP-mediated H2B acetylation. Nat. Struct. Mol. Biol. 21, 981–989 (2014).

  34. 34.

    , & The NAD biosynthesis pathway mediated by nicotinamide phosphoribosyltransferase regulates Sir2 activity in mammalian cells. J. Biol. Chem. 279, 50754–50763 (2004).

  35. 35.

    et al. Nutrient-sensitive mitochondrial NAD+ levels dictate cell survival. Cell 130, 1095–1107 (2007).

  36. 36.

    et al. Inhibition of nicotinamide phosphoribosyltransferase: cellular bioenergetics reveals a mitochondrial insensitive NAD pool. J. Biol. Chem. 285, 34106–34114 (2010).

  37. 37.

    , , & Pathways and subcellular compartmentation of NAD biosynthesis in human cells: from entry of extracellular precursors to mitochondrial NAD generation. J. Biol. Chem. 286, 21767–21778 (2011).

  38. 38.

    et al. Biosensor reveals multiple sources for mitochondrial NAD+. Science 352, 1474–1477 (2016).

  39. 39.

    et al. MacroH2A1 regulates the balance between self-renewal and differentiation commitment in embryonic and adult stem cells. Mol. Cell. Biol. 32, 1442–1452 (2012).

  40. 40.

    & Differential regulation and predictive potential of MacroH2A1 isoforms in colon cancer. Am. J. Pathol. 180, 2516–2526 (2012).

  41. 41.

    et al. MacroH2A1 isoforms are associated with epigenetic markers for activation of lipogenic genes in fat-induced steatosis. FASEB J. 29, 1676–1687 (2015).

  42. 42.

    et al. SIRT1-metabolite binding histone macroH2A1.1 protects hepatocytes against lipid accumulation. Aging (Albany NY) 6, 35–47 (2014).

  43. 43.

    et al. Genetic analysis of p38 MAP kinases in myogenesis: fundamental role of p38alpha in abrogating myoblast proliferation. EMBO J. 26, 1245–1256 (2007).

  44. 44.

    et al. A cellular model reflecting the phenotypic heterogeneity of mutant HRAS driven squamous cell carcinoma. Int. J. Cancer 139, 1106–1116 (2016).

  45. 45.

    et al. Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness. Nat. Struct. Mol. Biol. 19, 1139–1146 (2012).

  46. 46.

    et al. PML4 induces differentiation by Myc destabilization. Oncogene 26, 3415–3422 (2007).

  47. 47.

    et al. Hedgehog partial agonism drives Warburg-like metabolism in muscle and brown fat. Cell 151, 414–426 (2012).

  48. 48.

    & limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 20, 3705–3706 (2004).

  49. 49.

    et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11, 237 (2010).

  50. 50.

    , , & REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6, e21800 (2011).

  51. 51.

    & Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

  52. 52.

    et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952–1958 (2009).

Download references


We thank P. Muñoz Canoves for tools, training and advice; E. Gallardo (Institut de Recerca Hospital de la Santa Creu i Sant Pau, Barcelona, Spain) for primary human myoblasts; S. Samino for help with metabolomics analyses; S.-V. Forcales, A. Mikoč and the Ahel lab for helpful discussions; and the departments of pathology and biochemistry of the Hospital Universitari Germans Trias I Pujol (HGTP) for excellent support. This project was supported by MINECO (grants SAF2012-39749 and BFU2015-66559-P to M.B.; grant SAF2012-37427 to M.S.), AFM-Téléthon (grant 18738 to M.B.), the Marie Skłodowska Curie training network 'ChroMe' (grant H2020-MSCA-ITN-2015-675610 to M.B., A.G.L., O.Y. and J.A.P.), the Minerva Foundation (ARCHES award to T.P.), DZD (T.P.), the ERC (grants 281641 and 682679 to J.A.P.), DFG (grants SFB 646 and SFB 1064 to A.G.L.), the Wellcome Trust (grant 101794 to I.A.), Cancer Research UK (grant C35050/A22284 to I.A.), the Unity through Knowledge Fund (grant UKF 1B 2/13 to I.A.), ISCIII (grant PI15/00701 to P.M.G.-R.), MECD (FPU14/06542 to D.C.), AGAUR (FI fellowship to M.P.M.), and a Juan de la Cierva fellowship (JCI-2011-10831 to J.D.). Work in the Buschbeck lab is further supported by the Deutsche José Carreras Leukaemie Stiftung (DJCLS R 14/16), MINECO–ISCIII (PIE16/00011) and AGAUR (2014-SGR-35). Research at the IJC is supported by the 'La Caixa' Foundation, the Fundació Internacional Josep Carreras, Celgene Spain and the CERCA Programme/Generalitat de Catalunya.

Author information

Author notes

    • Melanija Posavec Marjanović

    Present address: Institute Ruđer Bošković Zagreb, Croatia.

    • Melanija Posavec Marjanović
    •  & Sarah Hurtado-Bagès

    These authors contributed equally to this work.


  1. Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain.

    • Melanija Posavec Marjanović
    • , Mònica Suelves
    •  & Marcus Buschbeck
  2. Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.

    • Melanija Posavec Marjanović
    •  & Sarah Hurtado-Bagès
  3. Josep Carreras Leukemia Research Institute (IJC), Campus ICO–Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.

    • Sarah Hurtado-Bagès
    • , Vanesa Valero
    • , Roberto Malinverni
    • , David Corujo
    • , Iva Guberovic
    • , Julien Douet
    •  & Marcus Buschbeck
  4. Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.

    • Maximilian Lassi
    •  & Raffaele Teperino
  5. German Center for Diabetes Research (DZD), Neuherberg, Germany.

    • Maximilian Lassi
    •  & Raffaele Teperino
  6. Université de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France.

    • Hélène Delage
    •  & Philippe Bouvet
  7. Metabolomics Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Spain.

    • Miriam Navarro
    •  & Oscar Yanes
  8. Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.

    • Miriam Navarro
    •  & Oscar Yanes
  9. Department of Physiological Sciences II, Faculty of Medicine, University of Barcelona, Barcelona, Spain.

    • Pau Gama-Perez
    •  & Pablo M Garcia-Roves
  10. Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.

    • Ivan Ahel
  11. Biomedical Center Munich (BMC)–Physiological Chemistry, Center for Integrated Protein Science Munich, Munich Cluster for Systems Neurology, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany.

    • Andreas G Ladurner
  12. Université de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France.

    • Philippe Bouvet
  13. Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

    • Raffaele Teperino
    •  & J Andrew Pospisilik


  1. Search for Melanija Posavec Marjanović in:

  2. Search for Sarah Hurtado-Bagès in:

  3. Search for Maximilian Lassi in:

  4. Search for Vanesa Valero in:

  5. Search for Roberto Malinverni in:

  6. Search for Hélène Delage in:

  7. Search for Miriam Navarro in:

  8. Search for David Corujo in:

  9. Search for Iva Guberovic in:

  10. Search for Julien Douet in:

  11. Search for Pau Gama-Perez in:

  12. Search for Pablo M Garcia-Roves in:

  13. Search for Ivan Ahel in:

  14. Search for Andreas G Ladurner in:

  15. Search for Oscar Yanes in:

  16. Search for Philippe Bouvet in:

  17. Search for Mònica Suelves in:

  18. Search for Raffaele Teperino in:

  19. Search for J Andrew Pospisilik in:

  20. Search for Marcus Buschbeck in:


M.P.M., R.T. and M.B. conceived the project; M.P.M., S.H.-B., M.S., P.B., I.A., A.G.L., P.M.G.-R., O.Y., J.A.P., R.T. and M.B. designed experiments and interpreted data; O.Y. contributed methods; M.P.M., S.H.-B., M.L., V.V., H.D., M.N., D.C., I.G., J.D. and P.G.-P. performed experiments; R.M. analyzed high-content data; and M.P.M., J.A.P., R.T. and M.B. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Raffaele Teperino or Marcus Buschbeck.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–4 and Supplementary Table 1.

  2. 2.

    Life Sciences Reporting Summary

  3. 3.

    Supplementary Data Set 1

    Uncropped images and blots.

Excel files

  1. 1.

    Supplementary Data Set 2

    Expression array data.

About this article

Publication history






Further reading