Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark

Nature Chemical Biology volume 10, pages 365–370 (2014)Cite this article

Subjects

Abstract

We report the identification of a new type of histone mark, lysine 2-hydroxyisobutyrylation (Khib), and identify the mark at 63 human and mouse histone Khib sites, including 27 unique lysine sites that are not known to be modified by lysine acetylation (Kac) and lysine crotonylation (Kcr). This histone mark was initially identified by MS and then validated by chemical and biochemical methods. Histone Khib shows distinct genomic distributions from histone Kac or histone Kcr during male germ cell differentiation. Using chromatin immunoprecipitation sequencing, gene expression analysis and immunodetection, we show that in male germ cells, H4K8hib is associated with active gene transcription in meiotic and post-meiotic cells. In addition, H4K8ac-associated genes are included in and constitute only a subfraction of H4K8hib-labeled genes. The histone Khib mark is conserved and widely distributed, has high stoichiometry and induces a large structural change. These findings suggest its critical role on the regulation of chromatin functions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Chemical structures for a possible PTM moiety caused by a mass shift of +86.0368 Da.
Figure 2: Verification of 2-hydroxyisobutyrylation at histone H4K77.
Figure 3: Histone Khib marks in eukaryotic cells.
Figure 4: H4K8hib is associated with genes with high transcriptional activity in male germ cells.

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

References

  1. Chi, P., Allis, C.D. & Wang, G.G. Covalent histone modifications—miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer 10, 457–469 (2010).

    Article  CAS  Google Scholar 

  2. Berger, S.L. The complex language of chromatin regulation during transcription. Nature 447, 407–412 (2007).

    Article  CAS  Google Scholar 

  3. Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6, 838–849 (2005).

    Article  CAS  Google Scholar 

  4. Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311–318 (2007).

    Article  CAS  Google Scholar 

  5. Montellier, E., Rousseaux, S., Zhao, Y. & Khochbin, S. Histone crotonylation specifically marks the haploid male germ cell gene expression program post-meiotic male-specific gene expression. Bioessays 34, 187–193 (2012).

    Article  CAS  Google Scholar 

  6. Montellier, E. et al. Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev. 27, 1680–1692 (2013).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Park, J. et al. SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol. Cell 50, 919–930 (2013).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Chen, Y., Chen, W., Cobb, M.H. & Zhao, Y. PTMap—a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc. Natl. Acad. Sci. USA 106, 761–766 (2009).

    Article  CAS  Google Scholar 

  12. Rohwerder, T. & Mueller, R.H. Biosynthesis of 2-hydroxyisobutyric acid (2-HIBA) from renewable carbon. Microb. Cell Fact. 9, 13 (2010).

    Article  Google Scholar 

  13. Kumps, A., Duez, P. & Mardens, Y. Metabolic, nutritional, iatrogenic, and artifactual sources of urinary organic acids: a comprehensive table. Clin. Chem. 48, 708–717 (2002).

    CAS  PubMed  Google Scholar 

  14. Freitas, M.A., Sklenar, A.R. & Parthun, M.R. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J. Cell. Biochem. 92, 691–700 (2004).

    Article  CAS  Google Scholar 

  15. Wisniewski, J.R., Zougman, A. & Mann, M. Nɛ formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function. Nucleic Acids Res. 36, 570–577 (2008).

    Article  CAS  Google Scholar 

  16. Olsen, J.V. et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signaling 3, ra3 (2010).

    Article  Google Scholar 

  17. Drogaris, P. et al. Histone deacetylase inhibitors globally enhance H3/H4 tail acetylation without affecting H3 lysine 56 acetylation. Sci. Rep. 2, 220 (2012).

    Article  Google Scholar 

  18. Gorovsky, M.A. et al. Histones and chromatin structure in Tetrahymena macro- and micronuclei. Cold Spring Harb. Symp. Quant. Biol. 42, 493–503 (1978).

    Article  CAS  Google Scholar 

  19. Morinière, J. et al. Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461, 664–668 (2009).

    Article  Google Scholar 

  20. Gaucher, J. et al. Bromodomain-dependent stage-specific male genome programming by Brdt. EMBO J. 31, 3809–3820 (2012).

    Article  CAS  Google Scholar 

  21. Turner, J.M.A. Meiotic sex chromosome inactivation. Development 134, 1823–1831 (2007).

    Article  CAS  Google Scholar 

  22. Namekawa, S.H. et al. Postmeiotic sex chromatin in the male germline of mice. Curr. Biol. 16, 660–667 (2006).

    Article  CAS  Google Scholar 

  23. Reynard, L.N. & Turner, J.M.A. Increased sex chromosome expression and epigenetic abnormalities in spermatids from male mice with Y chromosome deletions. J. Cell Sci. 122, 4239–4248 (2009).

    Article  CAS  Google Scholar 

  24. Maxwell, P.H. et al. The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature 399, 271–275 (1999).

    Article  CAS  Google Scholar 

  25. Katada, S., Imhof, A. & Sassone-Corsi, P. Connecting threads: epigenetics and metabolism. Cell 148, 24–28 (2012).

    Article  CAS  Google Scholar 

  26. Kaelin, W.G. & McKnight, S.L. Influence of metabolism on epigenetics and disease. Cell 153, 56–69 (2013).

    Article  CAS  Google Scholar 

  27. Garcia, B.A. et al. Chemical derivatization of histones for facilitated analysis by mass spectrometry. Nat. Protoc. 2, 933–938 (2007).

    Article  CAS  Google Scholar 

  28. Pivot-Pajot, C. et al. Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein. Mol. Cell. Biol. 23, 5354–5365 (2003).

    Article  CAS  Google Scholar 

  29. Kotaja, N. et al. Preparation, isolation and characterization of stage-specific spermatogenic cells for cellular and molecular analysis. Nat. Methods 1, 249–254 (2004).

    Article  CAS  Google Scholar 

  30. Zhang, Z. et al. Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol. 7, 58–63 (2011).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

S.K.'s group research is supported by Agence Nationale de la Recherche EpiSperm and Institut National du Cancer funds. E.M. was supported by a three-year grant from the French Ministry of Research and an Association pour la Recherche sur le Cancer fellowship for her fourth-year PhD.

Author information

Authors and Affiliations

  1. Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA

    Lunzhi Dai, Chao Peng, Zhike Lu, Yue Chen, Zhiyou Deng & Yingming Zhao

  2. INSERM, U823, Université Joseph Fourier–Grenoble 1, Institut Albert Bonniot, Faculté de Médecine, La Tronche, France

    Emilie Montellier, Alexandra Debernardi, Thierry Buchou, Sophie Rousseaux & Saadi Khochbin

  3. Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California–San Diego School of Medicine, La Jolla, California, USA

    Haruhiko Ishii, Fulai Jin & Bing Ren

  4. Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA

    Benjamin R Sabari & C David Allis

Authors
  1. Lunzhi Dai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chao Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Emilie Montellier
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhike Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yue Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Haruhiko Ishii
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alexandra Debernardi
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Thierry Buchou
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sophie Rousseaux
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Fulai Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Benjamin R Sabari
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Zhiyou Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. C David Allis
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Bing Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Saadi Khochbin
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Yingming Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.Z. and S.K. designed the experiments and wrote the paper. L.D. designed the experiments; synthesized chemicals; performed western blotting, immunoprecipitation, MS quantification and analysis; wrote the paper; and participated in other experiments. C.P. performed in vitro enzymatic assays. Y.C. and Z.D. performed MS analysis. E.M., Z.L., A.D., T.B., S.R., F.J., H.I. and B.R. performed immunofluorescence experiments, IHC and ChIP-Seq. B.R.S. and C.D.A. performed the Tetrahymena experiments.

Corresponding author

Correspondence to Yingming Zhao.

Ethics declarations

Competing interests

Y.Z. is a shareholder and a member of the scientific advisory board of PTM BioLabs, Co., Ltd. (Chicago, IL).

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–9, Supplementary Tables 1–5 and Supplementary Note. (PDF 3783 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dai, L., Peng, C., Montellier, E. et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat Chem Biol 10, 365–370 (2014). https://doi.org/10.1038/nchembio.1497

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.1497

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing