Abstract

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/).

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    1901–1921 Nobel Lectures. Including Presentation Speeches and Laureates' Biographies (Elsevier, Amsterdam, 1967).

  2. 2.

    , & Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl. Acad. Sci. USA 51, 786–794 (1964).

  3. 3.

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

  4. 4.

    et al. Unlocking the secrets of the genome. Nature 459, 927–930 (2009).

  5. 5.

    et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045–1048 (2010).

  6. 6.

    ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet. 10, 669–680 (2009).

  7. 7.

    , , , & The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies. Cell Struct. Funct. 33, 61–73 (2008).

  8. 8.

    Preparation of nuclear extracts from Drosophila embryos and in vitro transcription analysis. in Drosophila Protocols (W. Sullivan, M. Ashburner & R. Hawley, eds.) 553–557 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2000).

  9. 9.

    & Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).

  10. 10.

    et al. The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet. 6, e1001091 (2010).

  11. 11.

    et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376–381 (2009).

  12. 12.

    et al. Genome-wide analysis of polycomb targets in Drosophila melanogaster. Nat. Genet. 38, 700–705 (2006).

  13. 13.

    et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479–491 (2010).

Download references

Acknowledgements

This work was supported by US National Institutes of Health (NIH) modENCODE grants U01HG004270 to J.D.L. and U01HG004258 to G.H.K., and by the Reference Epigenome Roadmap project grant U01ES017166 to B.R. We thank H. Kimura (Kyoto University) and T. Jenuwein (Max Planck Institute of Immunobiology) for providing the noncommercial antibodies indicated in Supplementary Table 1 at no cost.

Author information

Author notes

    • Thea A Egelhofer
    • , Aki Minoda
    •  & Sarit Klugman

    These authors contributed equally to this work.

Affiliations

  1. Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA.

    • Thea A Egelhofer
    • , Andreas Rechtsteiner
    •  & Susan Strome
  2. Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA.

    • Aki Minoda
    •  & Gary H Karpen
  3. Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California, USA.

    • Aki Minoda
    •  & Gary H Karpen
  4. Ludwig Institute for Cancer Research, La Jolla, California, USA.

    • Sarit Klugman
    • , Samantha Kuan
    • , Ying Luu
    • , Queminh Ngo
    • , Bing Ren
    •  & R David Hawkins
  5. Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA.

    • Sarit Klugman
    • , Samantha Kuan
    • , Ying Luu
    • , Queminh Ngo
    • , Bing Ren
    •  & R David Hawkins
  6. Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.

    • Kyungjoon Lee
    • , Daniel S Day
    • , Peter V Kharchenko
    •  & Peter J Park
  7. The Gurdon Institute, University of Cambridge, Cambridge, UK.

    • Paulina Kolasinska-Zwierz
    • , Ming-Sin Cheung
    • , Isabel Latorre
    • , Anne Vielle
    •  & Julie Ahringer
  8. Department of Genetics, University of Cambridge, Cambridge, UK.

    • Paulina Kolasinska-Zwierz
    • , Ming-Sin Cheung
    • , Isabel Latorre
    • , Anne Vielle
    •  & Julie Ahringer
  9. Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA.

    • Artyom A Alekseyenko
    • , Andrey A Gorchakov
    •  & Mitzi I Kuroda
  10. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • Artyom A Alekseyenko
    • , Andrey A Gorchakov
    •  & Mitzi I Kuroda
  11. Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.

    • Sarah Gadel
    • , Tingting Gu
    • , Nicole C Riddle
    •  & Sarah C R Elgin
  12. Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey, USA.

    • Daniela Linder-Basso
    • , Yuri B Schwartz
    • , Gregory A Shanower
    •  & Vincenzo Pirrotta
  13. Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

    • Marc Perry
  14. Department of Biology, Carolina Center for Genome Sciences, Chapel Hill, North Carolina, USA.

    • Jason D Lieb
  15. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

    • Jason D Lieb

Authors

  1. Search for Thea A Egelhofer in:

  2. Search for Aki Minoda in:

  3. Search for Sarit Klugman in:

  4. Search for Kyungjoon Lee in:

  5. Search for Paulina Kolasinska-Zwierz in:

  6. Search for Artyom A Alekseyenko in:

  7. Search for Ming-Sin Cheung in:

  8. Search for Daniel S Day in:

  9. Search for Sarah Gadel in:

  10. Search for Andrey A Gorchakov in:

  11. Search for Tingting Gu in:

  12. Search for Peter V Kharchenko in:

  13. Search for Samantha Kuan in:

  14. Search for Isabel Latorre in:

  15. Search for Daniela Linder-Basso in:

  16. Search for Ying Luu in:

  17. Search for Queminh Ngo in:

  18. Search for Marc Perry in:

  19. Search for Andreas Rechtsteiner in:

  20. Search for Nicole C Riddle in:

  21. Search for Yuri B Schwartz in:

  22. Search for Gregory A Shanower in:

  23. Search for Anne Vielle in:

  24. Search for Julie Ahringer in:

  25. Search for Sarah C R Elgin in:

  26. Search for Mitzi I Kuroda in:

  27. Search for Vincenzo Pirrotta in:

  28. Search for Bing Ren in:

  29. Search for Susan Strome in:

  30. Search for Peter J Park in:

  31. Search for Gary H Karpen in:

  32. Search for R David Hawkins in:

  33. Search for Jason D Lieb in:

Contributions

J.A., A.A.A., M.-S.C., D.S.D., T.A.E., S.C.R.E., S.G., A.A.G., T.G., R.D.H., G.H.K., P.V.K., S. Klugman, P.K.-Z., S. Kuan, M.I.K., I.L., K.L., J.D.L., D.L.-B., Y.L., A.M., Q.N., P.J.P., M.P., V.P., A.R., B.R., N.C.R., Y.B.S., G.A.S., S.S. and A.V. designed, executed, and analyzed the experiments. T.A.E., R.D.H., G.H.K., J.D.L., A.M. and S.S. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Peter J Park or Gary H Karpen or R David Hawkins or Jason D Lieb.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figure 1

Excel files

  1. 1.

    Supplementary Table 1

    Tested antibodies and results.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nsmb.1972

Further reading