Abstract

Histones are highly covalently modified, but the functions of many of these modifications remain unknown. In particular, it is unclear how histone marks are coupled to cellular metabolism and how this coupling affects chromatin architecture. We identified histone H3 Lys14 (H3K14) as a site of propionylation and butyrylation in vivo and carried out the first systematic characterization of histone propionylation. We found that H3K14pr and H3K14bu are deposited by histone acetyltransferases, are preferentially enriched at promoters of active genes and are recognized by acylation-state-specific reader proteins. In agreement with these findings, propionyl-CoA was able to stimulate transcription in an in vitro transcription system. Notably, genome-wide H3 acylation profiles were redefined following changes to the metabolic state, and deletion of the metabolic enzyme propionyl-CoA carboxylase altered global histone propionylation levels. We propose that histone propionylation, acetylation and butyrylation may act in combination to promote high transcriptional output and to couple cellular metabolism with chromatin structure and function.

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References

  1. 1.

    , , , & SnapShot: histone modifications. Cell 159, 458–458.e1 (2014).

  2. 2.

    , & Bittersweet memories: linking metabolism to epigenetics through O-GlcNAcylation. Nat. Rev. Mol. Cell Biol 13, 312–321 (2012).

  3. 3.

    & Regulation of chromatin by histone modifications. Cell Res. 21, 381–395 (2011).

  4. 4.

    Chromatin modifications and their function. Cell 128, 693–705 (2007).

  5. 5.

    et al. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol. Cell. Proteomics 6, 812–819 (2007).

  6. 6.

    et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016–1028 (2011).

  7. 7.

    et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat. Chem. Biol. 10, 365–370 (2014).

  8. 8.

    et al. Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics 11, 100–107 (2012).

  9. 9.

    & Histone acylation beyond acetylation: terra incognita in chromatin biology. Cell J. 17, 1–6 (2015).

  10. 10.

    & Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains. Angew. Chem. Int. Edn Engl. 49, 6768–6772 (2010).

  11. 11.

    , & Protein lysine acylation and cysteine succination by intermediates of energy metabolism. ACS Chem. Biol. 7, 947–960 (2012).

  12. 12.

    & Influence of metabolism on epigenetics and disease. Cell 153, 56–69 (2013).

  13. 13.

    et al. ATP-citrate lyase links cellular metabolism to histone acetylation. Science 324, 1076–1080 (2009).

  14. 14.

    , & Histone acetyltransferases. Annu. Rev. Biochem. 70, 81–120 (2001).

  15. 15.

    , & Sodium butyrate inhibits histone deacetylation in cultured cells. Cell 14, 105–113 (1978).

  16. 16.

    & The language of covalent histone modifications. Nature 403, 41–45 (2000).

  17. 17.

    , & Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12, 7–18 (2011).

  18. 18.

    et al. Structure of p300 in complex with acyl-CoA variants. Nat. Chem. Biol. 13, 21–29 (2017).

  19. 19.

    & Structural basis for acyl-group discrimination by human Gcn5L2. Acta Crystallogr. D Struct. Biol. 72, 841–848 (2016).

  20. 20.

    , & KAT(ching) metabolism by the tail: insight into the links between lysine acetyltransferases and metabolism. ChemBioChem 12, 290–298 (2011).

  21. 21.

    , , & The human histone acetyltransferase P/CAF is a promiscuous histone propionyltransferase. ChemBioChem 9, 499–503 (2008).

  22. 22.

    et al. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J. 30, 249–262 (2011).

  23. 23.

    et al. The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription. Genes Dev. 28, 1999–2012 (2014).

  24. 24.

    , , , & Aberrant protein acylation is a common observation in inborn errors of acyl-CoA metabolism. J. Inherit. Metab. Dis. 37, 709–714 (2014).

  25. 25.

    , , , & Measurement of tissue acyl-CoAs using flow-injection tandem mass spectrometry: acyl-CoA profiles in short-chain fatty acid oxidation defects. Mol. Genet. Metab. 107, 679–683 (2012).

  26. 26.

    et al. Generation of a hypomorphic model of propionic acidemia amenable to gene therapy testing. Mol. Ther. 21, 1316–1323 (2013).

  27. 27.

    , , , & H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics 13, 424 (2012).

  28. 28.

    et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116–120 (2012).

  29. 29.

    et al. Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation. Mol. Cell 62, 194–206 (2016).

  30. 30.

    et al. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol. Cell 58, 203–215 (2015).

  31. 31.

    et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338, 349–354 (2012).

  32. 32.

    , , , & chromstaR: Tracking combinatorial chromatin state dynamics in space and time. Preprint at (2016).

  33. 33.

    et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).

  34. 34.

    et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 149, 214–231 (2012).

  35. 35.

    & of human bromodomains in chromatin biology and gene transcription. Curr. Opin. Drug Discov. Devel. 12, 659–665 (2009).

  36. 36.

    et al. Quantifying domain-ligand affinities and specificities by high-throughput holdup assay. Nat. Methods 12, 787–793 (2015).

  37. 37.

    et al. Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance. Sci. Adv. 1, e1500723 (2015).

  38. 38.

    et al. Jarid2 methylation via the PRC2 complex regulates H3K27me3 deposition during cell differentiation. Mol. Cell 57, 769–783 (2015).

  39. 39.

    , , , & Selective requirements for histone H3 and H4 N termini in p300-dependent transcriptional activation from chromatin. Mol. Cell 9, 811–821 (2002).

  40. 40.

    , , & Metabolic regulation of gene expression through histone acylations. Nat. Rev. Mol. Cell Biol. 18, 90–101 (2017).

  41. 41.

    Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12, 599–606 (1998).

  42. 42.

    , , , & How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007).

  43. 43.

    , , & Perceiving the epigenetic landscape through histone readers. Nat. Struct. Mol. Biol. 19, 1218–1227 (2012).

  44. 44.

    & Translating the histone code. Science 293, 1074–1080 (2001).

  45. 45.

    et al. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat. Genet. 45, 592–601 (2013).

  46. 46.

    & ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 396–420 (2011).

  47. 47.

    , & SnapShot: Chromatin remodeling: SWI/SNF. Cell 144, 310.e1 (2011).

  48. 48.

    et al. Dynamic competing histone H4 K5K8 acetylation and butyrylation are hallmarks of highly active gene promoters. Mol. Cell 62, 169–180 (2016).

  49. 49.

    et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006).

  50. 50.

    , & Propionic acidemia. in GeneReviews (eds. Pagon, R.A. et al.) (Seattle, 1993).

  51. 51.

    Measurement of protein by spectrophotometry at 205 nm. Anal. Biochem. 59, 277–282 (1974).

  52. 52.

    et al. Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell 152, 859–872 (2013).

  53. 53.

    , & Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007).

  54. 54.

    & Epigenetic changes in the brain: measuring global histone modifications. Methods Mol. Biol. 670, 263–274 (2011).

  55. 55.

    et al. Identification of a small TAF complex and its role in the assembly of TAF-containing complexes. PLoS One 2, e316 (2007).

  56. 56.

    & Sequential chromatin immunoprecipitation from animal tissues. Methods Enzymol. 376, 361–372 (2004).

  57. 57.

    et al. Standardizing chromatin research: a simple and universal method for ChIP-seq. Nucleic Acids Res. 44, e67 (2016).

  58. 58.

    et al. Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. eLife 3, e01632 (2014).

  59. 59.

    , , & Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

  60. 60.

    et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

  61. 61.

    & BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

  62. 62.

    , , , & deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).

  63. 63.

    , & Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).

  64. 64.

    et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

  65. 65.

    et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

  66. 66.

    , , , & Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).

  67. 67.

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

  68. 68.

    et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44 W1, W3–W10 (2016).

  69. 69.

    Venny: an interactive tool for comparing lists with Venn's diagrams. (2007).

  70. 70.

    et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

  71. 71.

    et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39, e35 (2011).

  72. 72.

    , & Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).

  73. 73.

    et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

  74. 74.

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

  75. 75.

    , & HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

  76. 76.

    & Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).

  77. 77.

    , & Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

  78. 78.

    & Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57, 289–300 (1995).

  79. 79.

    , & Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983).

  80. 80.

    Identifying chromatin readers using a SILAC-based histone peptide pull-down approach. Methods Enzymol. 512, 137–160 (2012).

  81. 81.

    , & Expression and purification of recombinant histones and nucleosome reconstitution. Methods Mol. Biol. 119, 1–16 (1999).

  82. 82.

    & Reconstitution and transcriptional analysis of chromatin in vitro. Methods Enzymol. 377, 460–474 (2004).

  83. 83.

    , , , & ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90, 145–155 (1997).

  84. 84.

    et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32, 503–518 (2008).

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Acknowledgements

We thank K. Bloom and M. Bennett (Children's Hospital Philadelphia) for Acads knockout tissues; A. Guenzel and M. Barry (Mayo Clinic) for Pcca knockout and gene-therapy-treated tissues; L. Arrigoni and J. Pospisilik for help with liver chromatin preparation; L. Tora (Institut de Genetique et de Biologie Moleculaire et Cellulaire, IGBMC) for baculoviruses expressing GCN5 and PCAF and for anti-GCN5 antibody; P. Laurette and I. Davidson (IGBMC) for antibodies against (P)BAF complex subunits; P. Eberling for peptide synthesis; S. Knapp (University of Frankfurt) for PFI-3 inhibitor; D. Widmann for initial analyses of data; and members of the Schneider laboratory for helpful discussions and reagents. M.C.-T. acknowledges support from the Helmholtz Association's Initiative and Networking Fund and from the University of Groningen (Rosalind Franklin Fellowship). Work by G. Meszaros and R.R. was supported by a European Research Council (ERC) starting grant (ERC-2011-StG, 281271-STRESSMETABOL). Work in the Schneider laboratory was supported by the Agence Nationale de Recherche (CoreAc), the DFG through SFB 1064, the Epigenomics of Common Diseases EpiTrio project and the Helmholtz Gesellschaft. Sequencing was performed by the IGBMC Microarray and Sequencing platform, a member of the 'France Génomique' consortium (ANR-10-INBS-0009).

Author information

Affiliations

  1. Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.

    • Adam F Kebede
    • , Stephanie Le Gras
    • , Gergo Meszaros
    • , Helena de Fatima Magliarelli
    • , Romeo Ricci
    • , Sylvain Daujat
    •  & Robert Schneider
  2. Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.

    • Adam F Kebede
    • , Florian Richter
    •  & Gerhard Mittler
  3. Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.

    • Anna Nieborak
    • , Lara Zorro Shahidian
    • , Diana Aguilar Gómez
    •  & Robert Schneider
  4. Goethe-Universität Fachbereich Medizin, Frankfurt, Germany.

    • Florian Richter
  5. Undergraduate Program in Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico.

    • Diana Aguilar Gómez
  6. Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.

    • Marijke P Baltissen
    •  & Michiel Vermeulen
  7. Université de Strasbourg, Strasbourg, France.

    • Gergo Meszaros
    •  & Romeo Ricci
  8. Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France.

    • Gergo Meszaros
    •  & Romeo Ricci
  9. European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.

    • Aaron Taudt
    •  & Maria Colomé-Tatché
  10. Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.

    • Aaron Taudt
    •  & Maria Colomé-Tatché
  11. Institut Curie, Paris, France.

    • Raphael Margueron
  12. Technical University Munich, Freising, Germany.

    • Maria Colomé-Tatché
  13. Ludwig-Maximilains-Universität München, Faculty of Biology, Munich, Germany.

    • Robert Schneider

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Contributions

A.F.K. and R.S. conceived the project. A.F.K. characterized antibodies, performed most of the ChIP, knockdown and peptide pulldown experiments and analyzed data. A.N. contributed to antibody characterization and knockdown experiments, and performed GAL4 recruitment ChIP and luciferase assays. L.Z.S. performed in vitro transcription experiments with the help of R.M. S.L.G. and D.A.G. performed analyses of ChIP and RNA-seq data. F.R. and G. Mittler performed and analyzed histone-modification mass spectrometry experiments. M.P.B. and M.V. performed and analyzed peptide-pulldown mass spectrometry experiments. G. Meszaros, H.F.M. and R.R. contributed to animal fasting and liver cross-linking experiments. A.T. and M.C.-T. performed ChIP–seq data analyses. A.F.K., S.D. and R.S. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Robert Schneider.

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https://doi.org/10.1038/nsmb.3490

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