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Robust 4C-seq data analysis to screen for regulatory DNA interactions

Nature Methods volume 9, pages 969–972 (2012)Cite this article

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Abstract

Regulatory DNA elements can control the expression of distant genes via physical interactions. Here we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq). Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.

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Figure 1: 4C-seq.
Figure 2: Promoter–locus control region (LCR) interactions in the active β-globin cluster.

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Gene Expression Omnibus

Change history

  • 21 September 2012

    In the version of this article initially published online, the name of Christian Valdes-Quezada was misspelled as Christian Valdes Quezada. The error has been corrected for the print, PDF and HTML version of this article.

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Acknowledgements

We would like to thank R. Palstra, E. Yaffe and other members of our labs for help and input, G. Geeven for testing the 4C-seq pipeline and H.T. Timmers (Netherlands Proteomics Centre and University Medical Center Utrecht) and J.P.P. Meijerink (Erasmus Medical Center-Sophia Children′s Hospital) for providing cells. This work was supported by grants from the Modelling Hepatocellular Carcinoma (MODHEP) Seventh Framework Program (FP7) collaborative project to W.d.L. and A.T., grants from the Dutch Scientific Organization (NWO) (91204082 and 935170621), a European Research Council Starting Grant (209700, '4C') and InteGeR FP7 Marie Curie Initial Training Networks contract (no. PITN-GA-2007-214902) to W.d.L., and the Israeli Science Foundation integrated technologies grant to A.T.

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Author notes

  1. Harmen J G van de Werken and Gilad Landan: These authors contributed equally to this work.

Authors and Affiliations

  1. Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands

    Harmen J G van de Werken, Sjoerd J B Holwerda, Petra Klous, Erik Splinter, Yuva Öz, Britta A M Bouwman, Marjon J A M Verstegen, Elzo de Wit & Wouter de Laat

  2. University Medical Center Utrecht, Utrecht, The Netherlands

    Harmen J G van de Werken, Sjoerd J B Holwerda, Petra Klous, Erik Splinter, Yuva Öz, Britta A M Bouwman, Marjon J A M Verstegen, Elzo de Wit & Wouter de Laat

  3. Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel

    Gilad Landan, Michael Hoichman, Ran Chachik & Amos Tanay

  4. Department of Biological Regulation, Weizmann Institute, Rehovot, Israel

    Gilad Landan, Michael Hoichman, Ran Chachik & Amos Tanay

  5. Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México Distrito Federal, Mexico

    Christian Valdes-Quezada

Authors
  1. Harmen J G van de Werken
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  2. Gilad Landan
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Contributions

H.J.G.v.d.W. designed, performed and analyzed experiments and wrote the manuscript; E.S. helped design experiments; G.L. helped design and analyze experiments and wrote the manuscript; P.K., S.J.B.H., B.A.M.B., M.J.A.M.V., Y.Ö. and C.V.-Q. performed experiments; M.H., R.C. and E.d.W. helped analyze experiments; and A.T. and W.d.L. designed experiments, supervised the project and wrote the manuscript.

Corresponding authors

Correspondence to Amos Tanay or Wouter de Laat.

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The authors declare no competing financial interests.

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Supplementary Figures 1–15 and Supplementary Tables 1–4 (PDF 15411 kb)

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van de Werken, H., Landan, G., Holwerda, S. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 9, 969–972 (2012). https://doi.org/10.1038/nmeth.2173

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