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.

  • Resource
  • Published:

An assessment of histone-modification antibody quality

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/).

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

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

Figure 1: Representative western assays and results.
Figure 2: Representative dot blot assays and results.
Figure 3: ChIP-chip and ChIP-seq.

Similar content being viewed by others

References

  1. Sourkes, T.L. 1901–1921 Nobel Lectures. Including Presentation Speeches and Laureates' Biographies (Elsevier, Amsterdam, 1967).

  2. Allfrey, V.G., Faulkner, R. & Mirsky, A.E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl. Acad. Sci. USA 51, 786–794 (1964).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Kimura, H., Hayashi-Takanaka, Y., Goto, Y., Takizawa, N. & Nozaki, N. The organization of histone H3 modifications as revealed by a panel of specific monoclonal antibodies. Cell Struct. Funct. 33, 61–73 (2008).

    Article  CAS  Google Scholar 

  8. Pazin, M. 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. Sambrook, J. & Russell, D. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).

  10. Rechtsteiner, A. 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).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

Authors and Affiliations

Authors

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.

Corresponding authors

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

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1 (PDF 250 kb)

Supplementary Table 1

Tested antibodies and results. (XLS 130 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Egelhofer, T., Minoda, A., Klugman, S. et al. An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18, 91–93 (2011). https://doi.org/10.1038/nsmb.1972

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

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

This article is cited by

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