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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Nature Genetics volume 46, pages 205–212 (2014)Cite this article

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Abstract

Gene expression during development and differentiation is regulated in a cell- and stage-specific manner by complex networks of intergenic and intragenic cis-regulatory elements whose numbers and representation in the genome far exceed those of structural genes. Using chromosome conformation capture, it is now possible to analyze in detail the interaction between enhancers, silencers, boundary elements and promoters at individual loci, but these techniques are not readily scalable. Here we present a high-throughput approach (Capture-C) to analyze cis interactions, interrogating hundreds of specific interactions at high resolution in a single experiment. We show how this approach will facilitate detailed, genome-wide analysis to elucidate the general principles by which cis-acting sequences control gene expression. In addition, we show how Capture-C will expedite identification of the target genes and functional effects of SNPs that are associated with complex diseases, which most frequently lie in intergenic cis-acting regulatory elements.

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Figure 1: Interaction profile viewed fromthe α-globin gene promoters.
Figure 2: Validation of the Capture-C technique.
Figure 3: Characterization of the Tal1 and Slc25a37 loci.
Figure 4: Using Capture-C to determine the effect of distal SNPs on gene regulation.

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Acknowledgements

We thank J. Davies and P. Piazza for technical suggestions. We thank M. Suciu, B. Graham and T. Milne for suggestions and critically reading the manuscript. We thank Z.-P. Han and J. Telenius for computational support. We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (funded by Wellcome Trust grant reference 090532/Z/09/Z and MRC Hub grant G0900747 91070) for the generation of the sequencing data. This work was supported by the MRC (UK) and by the Blood theme within Oxford Biomedical Research Centre (which is part of the National Institute for Health Research Biomedical Research Centres scheme). We also thank EpiGeneSys for support.

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Authors and Affiliations

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

    Jim R Hughes, Nigel Roberts, Deborah Hay, Magnus Lynch, Marco De Gobbi, Richard Gibbons & Douglas R Higgs

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

    Simon McGowan, Eleni Giannoulatou & Stephen Taylor

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Contributions

J.R.H., D.R.H. and R.G. designed experiments. J.R.H., N.R., D.H., M.L. and M.D.G. performed experiments. J.R.H. performed bioinformatic analysis. E.G. performed statistical analysis. S.M. and S.T. provided bioinformatic support. J.R.H. and D.R.H. wrote the manuscript.

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Correspondence to Jim R Hughes or Douglas R Higgs.

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Hughes, J., Roberts, N., McGowan, S. et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 46, 205–212 (2014). https://doi.org/10.1038/ng.2871

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