Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

  • Mowei Zhou
  • Si Wu
  • David L. Stenoien
  • Zhaorui Zhang
  • Lanelle Connolly
  • Michael Freitag
  • Ljiljana Paša-Tolić
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1507)

Abstract

Top-down mass spectrometry is a valuable tool for understanding gene expression through characterization of combinatorial histone post-translational modifications (i.e., histone code). In this protocol, we describe a top-down workflow that employs liquid chromatography (LC) coupled to mass spectrometry (MS), for fast global profiling of changes in histone proteoforms, and apply LCMS top-down approach for comparative analysis of a wild-type and a mutant fungal species. The proteoforms exhibiting differential abundances can be subjected to further targeted studies by other MS or orthogonal (e.g., biochemical) assays. This method can be generally adapted for screening of changes in histone modifications between samples such as wild type vs. mutant or healthy vs. diseased.

Key words

Histone Post-translational modification Liquid chromatography Mass spectrometry Top-down Screening 

References

  1. 1.
    Smith LM, Kelleher NL (2013) Proteoform: a single term describing protein complexity. Nat Methods 10(3):186–187. doi:10.1038/nmeth.2369 CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Han X, Aslanian A, Yates Iii JR (2008) Mass spectrometry for proteomics. Curr Opin Chem Biol 12(5):483–490. doi:10.1016/j.cbpa.2008.07.024 CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Yates JR, Ruse CI, Nakorchevsky A (2009) Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 11(1):49–79. doi:10.1146/annurev-bioeng-061008-124934 CrossRefPubMedGoogle Scholar
  4. 4.
    Bowman GD, Poirier MG (2015) Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 115(6):2274–2295. doi:10.1021/cr500350x CrossRefPubMedGoogle Scholar
  5. 5.
    Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45CrossRefPubMedGoogle Scholar
  6. 6.
    Jenuwein T, Allis CD (2001) Translating the histone code. Science 293(5532):1074–1080. doi:10.1126/science.1063127 CrossRefPubMedGoogle Scholar
  7. 7.
    Chi P, Allis CD, Wang GG (2010) Covalent histone modifications—miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10(7):457–469. doi:10.1038/nrc2876 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Greer EL, Shi Y (2012) Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 13(5):343–357. doi:10.1038/nrg3173 CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Portela A, Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28(10):1057–1068. doi:10.1038/nbt.1685 CrossRefPubMedGoogle Scholar
  10. 10.
    Yuan Z-F, Arnaudo AM, Garcia BA (2014) Mass spectrometric analysis of histone proteoforms. Annu Rev Anal Chem 7(1):113–128. doi:10.1146/annurev-anchem-071213-015959 CrossRefGoogle Scholar
  11. 11.
    Moradian A, Kalli A, Sweredoski MJ, Hess S (2014) The top-down, middle-down, and bottom-up mass spectrometry approaches for characterization of histone variants and their post-translational modifications. Proteomics 14(4-5):489–497. doi:10.1002/pmic.201300256 CrossRefPubMedGoogle Scholar
  12. 12.
    Connolly LR, Smith KM, Freitag M (2013) The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet 9(10), e1003916. doi:10.1371/journal.pgen.1003916 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Tian Z, Tolic N, Zhao R, Moore R, Hengel S, Robinson E, Stenoien D, Wu S, Smith R, Pasa-Tolic L (2012) Enhanced top-down characterization of histone post-translational modifications. Genome Biol 13(10):R86. doi:10.1186/gb-2012-13-10-r86 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Wu S, Lourette NM, Tolić N, Zhao R, Robinson EW, Tolmachev AV, Smith RD, Paša-Tolić L (2009) An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications. J Proteome Res 8(3):1347–1357. doi:10.1021/pr800720d CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    LaMarche BL, Orton DJ, Clark DA, Ryan JD, Hopkins DF, Anderson GA, Moore RJ, Smith RD LC control software for maximum flexibility and rapid automation of new mode of operation. In: 59rd ASMS conference on mass spectrometry and allied topics, Denvor, CO, 2011Google Scholar
  16. 16.
    Shechter D, Dormann HL, Allis CD, Hake SB (2007) Extraction, purification and analysis of histones. Nat Protoc 2(6):1445–1457CrossRefPubMedGoogle Scholar
  17. 17.
    Pesavento JJ, Garcia BA, Streeky JA, Kelleher NL, Mizzen CA (2007) Mild performic acid oxidation enhances chromatographic and top down mass spectrometric analyses of histones. Mol Cell Proteomics 6(9):1510–1526. doi:10.1074/mcp.M600404-MCP200 CrossRefPubMedGoogle Scholar
  18. 18.
    Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA (2012) Protein identification using top-down spectra. Mol Cell Proteomics 11(6). doi:10.1074/mcp.M111.008524Google Scholar
  19. 19.
    LeDuc RD, Taylor GK, Kim Y-B, Januszyk TE, Bynum LH, Sola JV, Garavelli JS, Kelleher NL (2004) ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. Nucleic Acids Res 32(suppl 2):W340–W345. doi:10.1093/nar/gkh447 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Sidoli S, Lin S, Karch KR, Garcia BA (2015) Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry. Anal Chem 87(6):3129–3133. doi:10.1021/acs.analchem.5b00072 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Mowei Zhou
    • 1
  • Si Wu
    • 1
    • 2
  • David L. Stenoien
    • 1
  • Zhaorui Zhang
    • 1
  • Lanelle Connolly
    • 3
  • Michael Freitag
    • 3
  • Ljiljana Paša-Tolić
    • 1
  1. 1.Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of OklahomaNormanUSA
  3. 3.Department of Biochemistry and Biophysics, Center for Genome Research and BiocomputingOregon State UniversityCorvallisUSA

Personalised recommendations