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Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Nature Methods volume 13, pages 74–80 (2016)Cite this article

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Abstract

Methods for analyzing chromosome conformation in mammalian cells are either low resolution or low throughput and are technically challenging. In next-generation (NG) Capture-C, we have redesigned the Capture-C method to achieve unprecedented levels of sensitivity and reproducibility. NG Capture-C can be used to analyze many genetic loci and samples simultaneously. High-resolution data can be produced with as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. The method is straightforward to perform and should greatly facilitate the investigation of many questions related to gene regulation as well as the functional dissection of traits examined in genome-wide association studies.

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Figure 1: Overview of the method.
Figure 2: Single and double oligonucleotide capture.
Figure 3: Identification of regulatory elements using comparative analysis.
Figure 4: SNP-specific interaction profiles.

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Acknowledgements

J.O.J.D. thanks the Wellcome Trust for funding his work (Wellcome Trust Clinical Research Training Fellowship reference 098931/Z/12/Z). The work was also supported by a Wellcome Trust Strategic Award (reference 106130/Z/14/Z) and the Medical Research Council (MRC Core Funding and Centenary Award reference 4050189188). We thank E. Repapi for statistical advice and L. Hanssen, M. Oudelaar, D. Jeziorska, B. Graham, M. Kassouf, M. Suciu, H. Long, S. Pasricha, V. Buckle, T. Milne, T. Fulga, T. Sauka-Spengler, D. Downes and A. Drakesmith for their critique of the manuscript. We thank S. Thongjuea for discussions on analysis.

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Authors and Affiliations

  1. Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK

    James O J Davies, Jelena M Telenius, Nigel A Roberts, Douglas R Higgs & Jim R Hughes

  2. Computational Biology Research Group, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK

    Simon J McGowan & Stephen Taylor

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  1. James O J Davies
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  7. Jim R Hughes
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Contributions

J.O.J.D. performed the experiments, analyzed the data and wrote the manuscript. J.R.H. designed the experiments, assisted with the bioinformatic analysis and wrote the manuscript. N.A.R. assisted with the experiments. J.M.T. analyzed the data. S.J.M. and S.T. assisted with the bioinformatics analysis and prepared the software for public release. D.R.H. wrote the manuscript.

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Correspondence to Jim R Hughes.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–22 and Supplementary Note (PDF 20583 kb)

Supplementary Data

NG Capture-C supplementary data file (XLSX 55 kb)

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Davies, J., Telenius, J., McGowan, S. et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 13, 74–80 (2016). https://doi.org/10.1038/nmeth.3664

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