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Pervasive combinatorial modification of histone H3 in human cells

Nature Methods volume 4, pages 487–489 (2007)Cite this article

Abstract

We developed a platform using hydrophilic interaction chromatography and high-resolution tandem mass spectrometry (MS) for analyses of histone H3 that allows comprehensive characterization of 'histone codes' at the molecular level. We identified over 150 differentially modified forms of histone H3.2 in asynchronously grown and butyrate-treated HeLa cells, revealing pervasive combinatorial modification previously unaccounted for by other techniques and providing a clarified estimate of the molecular diversity of histone H3 in mammals.

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Figure 1: MS-based platform for the detection of individual histone H3 codes.
Figure 2: Schematic representation of the acetylation patterns observed on histone H3.2.

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Acknowledgements

Funding from the US National Institutes of Health (NIH; GM 067193), the Packard Foundation, the Alfred P. Sloan Foundation and a 2004 Camille Dreyfus Teacher-Scholar Award from the Dreyfus Foundation to N.L.K., from the Roy J. Carver Charitable Trust (04-76) and the March of Dimes (Basil O'Connor Scholar Award 5-FY05-1232) to C.A.M., and from the Institute of Genomic Biology at the University of Illinois and the NIH (1 F32 GM 078942-01) to B.A.G. are gratefully acknowledged. J.J.P. is a recipient of an NIH Institutional National Research Service award in Molecular Biophysics (5T32 GM 08276).

Author information

Authors and Affiliations

  1. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    Benjamin A Garcia, Craig A Mizzen & Neil L Kelleher

  2. Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    James J Pesavento

  3. Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    Craig A Mizzen

  4. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    Neil L Kelleher

Authors
  1. Benjamin A Garcia
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  2. James J Pesavento
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  3. Craig A Mizzen
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  4. Neil L Kelleher
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Contributions

B.A.G. conducted experiments, interpreted data and wrote paper; J.J.P. conducted experiments; C.A.M. designed experiments and wrote paper; N.L.K. designed experiments, interpreted data and wrote paper.

Corresponding authors

Correspondence to Craig A Mizzen or Neil L Kelleher.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

HILIC fractionation and mass spectrometry resolves isomeric differently modified histone H3 codes. (PDF 51 kb)

Supplementary Fig. 2

HILIC separation and mass spectrometry reveals interdependence of histone H3K4 methylation with acetylation. (PDF 59 kb)

Supplementary Fig. 3

Semi-quantitative determination of the relative abundances for the species at 5408 m/z from asynchronously grown and butyrate treated cells. (PDF 79 kb)

Supplementary Table 1

Histone H3.2 species separated by HILIC and characterized by ECD. (PDF 47 kb)

Supplementary Table 2

ECD fragment ions observed from histone H3.2 species from selected fractions 1-10. (PDF 122 kb)

Supplementary Table 3

Semi-quantitative relative abundance values for selected histone H3.2 species from asynchronously grown and butyrate treated HeLa cells separated by HILIC and characterized by ECD. (PDF 10 kb)

Supplementary Discussion (PDF 12 kb)

Supplementary Methods (PDF 27 kb)

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Garcia, B., Pesavento, J., Mizzen, C. et al. Pervasive combinatorial modification of histone H3 in human cells. Nat Methods 4, 487–489 (2007). https://doi.org/10.1038/nmeth1052

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