Skip to main content

Thank you for visiting 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.

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq


Chromatin immunoprecipitation (ChIP) combined with high-throughput sequencing (ChIP-seq) has become the gold standard for whole-genome mapping of protein-DNA interactions. However, conventional ChIP protocols necessitate the use of large numbers of cells, and library preparation steps associated with current high-throughput sequencing platforms require substantial amounts of DNA; both of these factors preclude the application of ChIP-seq technology to many biologically important but rare cell types. Here we describe a nano-ChIP-seq protocol that combines a high-sensitivity small-scale ChIP assay and a tailored procedure for generating high-throughput sequencing libraries from scarce amounts of ChIP DNA. In terms of the numbers of cells required, the method provides two to three orders of magnitude of improvement over the conventional ChIP-seq method and the entire procedure can be completed within 4 d.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Schematic of nano-ChIP-seq library preparation method.
Figure 2: The sonication setup with the Branson 250.


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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Dahl, J.A. & Collas, P. Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynamics of developmentally regulated genes in human carcinoma cells. Stem Cells 25, 1037–1046 (2007).

    CAS  Article  PubMed  Google Scholar 

  3. Acevedo, L.G. et al. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques 43, 791–797 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. O'Neill, L.P., VerMilyea, M.D. & Turner, B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat. Genet. 38, 835–841 (2006).

    CAS  Article  PubMed  Google Scholar 

  5. Attema, J.L. et al. Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl. Acad. Sci. USA 104, 12371–12376 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. Goren, A. et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat. Methods 7, 47–49 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Adli, M., Zhu, J. & Bernstein, B.E. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods 7, 615–618 (2010).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Shankaranarayanan, P. et al. Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat. Methods 8, 565–567 (2011).

    CAS  Article  PubMed  Google Scholar 

  9. Dahl, J.A. & Collas, P. A rapid micro chromatin immunoprecipitation assay (microChIP). Nat. Protoc. 3, 1032–1045 (2008).

    CAS  Article  PubMed  Google Scholar 

  10. Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327–334 (2001).

    CAS  Article  PubMed  Google Scholar 

Download references


We acknowledge all the members of the Bernstein Lab for constructive discussions during the method development. We thank M. Coyne, S. Furuyama, S. Gillespie and N.A. Okan for their critical reading of the manuscript and J. Zhu, N. Shoresh and T. Mikkelsen for computational assistance. This research was supported by funds from the Starr Cancer Consortium, a Charles E. Culpeper Scholarship, the US National Human Genome Research Institute, the National Institutes of Health Roadmap for Epigenomics and the National Heart, Lung and Blood Institute.


M.A. and B.E.B. designed the method and analyzed the data. M.A. performed the experiments and wrote the manuscript.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Mazhar Adli or Bradley E Bernstein.

Ethics declarations

Competing interests

M.A. and B.E.B. have filed a patent application describing the methods presented here. Patent application #: 12 / 699508 (USA)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Adli, M., Bernstein, B. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc 6, 1656–1668 (2011).

Download citation

  • Published:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


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