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Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails

  • Kevin A. Janssen
  • Mariel Coradin
  • Congcong Lu
  • Simone Sidoli
  • Benjamin A. GarciaEmail author
Focus: Protein Post-translational Modifications: Research Article

Abstract

The analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has been critical to the advancement of the field of epigenetics. The most sensitive and accurate workflow is similar to the canonical proteomics analysis workflow (bottom-up MS), where histones are digested into short peptides (4-20 aa) and quantitated in extracted ion chromatograms. However, this limits the ability to detect even very common co-occurrences of modifications on histone proteins, preventing biological interpretation of PTM crosstalk. By digesting with GluC rather than trypsin, it is possible to produce long polypeptides corresponding to intact histone N-terminal tails (50-60 aa), where most modifications reside. This middle-down MS approach is used to study distant PTM co-existence. However, the most sensitive middle-down workflow uses weak cation exchange-hydrophilic interaction chromatography (WCX-HILIC), which is less robust than conventional reversed-phase chromatography. Additionally, since the buffer systems for middle-down and bottom-up proteomics differ substantially, it is cumbersome to toggle back and forth between both experimental setups on the same LC system. Here, we present a new workflow using porous graphitic carbon (PGC) as a stationary phase for histone analysis where bottom-up and middle-down sized histone peptides can be analyzed simultaneously using the same reversed-phase buffer setup. By using this protocol for middle-down sized peptides, we identified 406 uniquely modified intact histone tails and achieved a correlation of 0.85 between PGC and WCX-HILIC LC methods. Together, our method facilitates the analysis of single and combinatorial histone PTMs with much simpler applicability for conventional proteomics labs than the state-of-the-art middle-down MS.

Keywords

Histones Epigenetics Proteomics Middle-down PTMs Chromatography 

Notes

Acknowledgements

We gratefully acknowledge funding from NIH grants GM110174, AI118891, and CA196539.

Supplementary material

13361_2019_2303_MOESM1_ESM.docx (1.2 mb)
ESM 1 (DOCX 1233 kb)

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Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  • Kevin A. Janssen
    • 1
    • 2
  • Mariel Coradin
    • 1
    • 2
  • Congcong Lu
    • 2
  • Simone Sidoli
    • 2
    • 3
  • Benjamin A. Garcia
    • 1
    • 2
    Email author
  1. 1.Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaUSA
  2. 2.Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaUSA
  3. 3.Department of BiochemistryAlbert Einstein College of MedicineNew YorkUSA

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