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Single-tube linear DNA amplification (LinDA) for robust ChIP-seq

Nature Methods volume 8, pages 565–567 (2011)Cite this article

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Abstract

Genome-wide profiling of transcription factors based on massive parallel sequencing of immunoprecipitated chromatin (ChIP-seq) requires nanogram amounts of DNA. Here we describe a high-fidelity, single-tube linear DNA amplification method (LinDA) for ChIP-seq and reChIP-seq with picogram DNA amounts obtained from a few thousand cells. This amplification technology will facilitate global analyses of transcription-factor binding and chromatin with very small cell populations, such as stem or cancer-initiating cells.

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Figure 1: Linear amplification of DNA.
Figure 2: ReChIP of RARγ-RXRα heterodimer using LinDA.

References

  1. Acevedo, L.G. et al. Biotechniques 43, 791–797 (2007).

    Article  CAS  Google Scholar 

  2. O'Neill, L.P., VerMilyea, M.D. & Turner, B.M. Nat. Genet. 38, 835–841 (2006).

    Article  CAS  Google Scholar 

  3. Dahl, J.A. & Collas, P. Nat. Protoc. 3, 1032–1045 (2008).

    Article  CAS  Google Scholar 

  4. O'Geen, H., Nicolet, C.M., Blahnik, K., Green, R. & Farnham, P.J. Biotechniques 41, 577–580 (2006).

    Article  CAS  Google Scholar 

  5. Pfeifer, G.P., Steigerwald, S.D., Mueller, P.R., Wold, B. & Riggs, A.D. Science 246, 810–813 (1989).

    Article  CAS  Google Scholar 

  6. Pinard, R. et al. BMC Genomics 7, 216 (2006).

    Article  Google Scholar 

  7. Talseth-Palmer, B.A., Bowden, N.A., Hill, A., Meldrum, C. & Scott, R.J. BMC Res. Notes 1, 56 (2008).

    Article  Google Scholar 

  8. Goren, A. et al. Nat. Methods 7, 47–49 (2010).

    Article  CAS  Google Scholar 

  9. Liu, C.L., Schreiber, S.L. & Bernstein, B.E. BMC Genomics 4, 19 (2003).

    Article  CAS  Google Scholar 

  10. Adli, M., Zhu, J. & Bernstein, B.E. Nat. Methods 7, 615–618 (2010).

    Article  CAS  Google Scholar 

  11. van Bakel, H. et al. Nucleic Acids Res. 36, e21 (2008).

    Article  Google Scholar 

  12. Liu, C.L., Bernstein, B.E. & Schreiber, S.L. Cold Spring Harb. Protoc. pdb.top42 (2008).

  13. Ceschin, D.G. et al. Genes Dev. (in the press).

  14. Zhang, Y. et al. Genome Biol. 9, R137 (2008).

    Article  Google Scholar 

  15. Ye, T. et al. Nucleic Acids Res. 39, e35 (2011).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank B. Jost, S. Vicaire and S. Le Gras for Illumina sequencing and mapping to the genomes, W. van Gool for help in the data analysis, A. Krebs for help with seqMINER and D. Ceschin advice on statistics and for critical reading of the manuscript. P.S. is a postdoc at the Ligue Nationale Contre le Cancer; M.W. is supported by fellowships of the Association pour le Recherche sur le Cancer and the Fondation pour la Recherche Médicale. This work was supported by funds from the Ligue Nationale Contre le Cancer (laboratoire labelisé) and European Community contracts LSHC-CT-2005-518417 'EPITRON', LSHG-CT2005-018882 'X-TRA-NET', LSHM-CT2005-018652 'CRESCENDO' and HEALTH-F4-2009-221952 'ATLAS'.

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Authors and Affiliations

  1. Department of Cancer Biology, Institute of Genetics and Molecular and Cellular Biology, Strasbourg-Illkirch, France

    Pattabhiraman Shankaranarayanan, Marco-Antonio Mendoza-Parra, Mannu Walia & Hinrich Gronemeyer

  2. Beijing Genome Institute, Guangdong, China

    Li Wang & Ning Li

  3. Wageningen University and Research Center–Plant Breeding, Wageningen, The Netherlands

    Luisa M Trindade

Authors
  1. Pattabhiraman Shankaranarayanan
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  2. Marco-Antonio Mendoza-Parra
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  3. Mannu Walia
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  4. Li Wang
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  5. Ning Li
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  6. Luisa M Trindade
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  7. Hinrich Gronemeyer
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Contributions

P.S., L.M.T. and H.G. designed and optimized LinDA. M.-A.M.-P. performed the F9-cell experiments and did the bioinformatics analysis with P.S., and M.W. did the H3396-cell experiments. N.L. and L.W. performed the Illumina HiSeq 2000 sequencing and mapping to hg19 human genome assembly. H.G. and P.S. wrote the main text of the manuscript, which M.-A.M.-P. and L.M.T. corrected and improved; P.S. and L.M.T. wrote the Online Methods section.

Corresponding author

Correspondence to Hinrich Gronemeyer.

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Competing interests

H.G., P.S. and L.M.T. filed a patent application describing the methods presented here (European patent EP11305531.3).

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Supplementary Figures 1–6 and Supplementary Tables 1–2 (PDF 880 kb)

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Shankaranarayanan, P., Mendoza-Parra, MA., Walia, M. et al. Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat Methods 8, 565–567 (2011). https://doi.org/10.1038/nmeth.1626

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