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FISH-ing for captured contacts: towards reconciling FISH and 3C

Nature Methods volume 14, pages 673–678 (2017)Cite this article

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Abstract

Chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) are two widely used technologies that provide distinct readouts of 3D chromosome organization. While both technologies can assay locus-specific organization, how to integrate views from 3C, or genome-wide Hi-C, and FISH is far from solved. Contact frequency, measured by Hi-C, and spatial distance, measured by FISH, are often assumed to quantify the same phenomena and used interchangeably. Here, however, we demonstrate that contact frequency is distinct from average spatial distance, both in polymer simulations and in experimental data. Performing a systematic analysis of the technologies, we show that this distinction can create a seemingly paradoxical relationship between 3C and FISH, both in minimal polymer models with dynamic looping interactions and in loop-extrusion simulations. Together, our results indicate that cross-validation of Hi-C and FISH should be carefully designed, and that jointly considering contact frequency and spatial distance is crucial for fully understanding chromosome organization.

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Figure 1: Illustrated relationship between 3C and FISH.
Figure 2: Experimental data demonstrate the complex relationship between Hi-C and FISH.
Figure 3: Simulations demonstrate the effect of introducing a single dynamic loop.
Figure 4: Simulations clarify the complex relationship between contact frequency and median spatial distance.
Figure 5: Loop-extrusion simulations can display divergent contact frequency and spatial distance.

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Acknowledgements

The authors thank A. Goloborodko for thoughtful comments regarding the statistical mechanics analogy of re-weighting loop conformations, G. Nir for helpful discussions regarding imaging, and anonymous reviewers for thoughtful and detailed feedback. The authors also thank J. Dekker and other members of the UMass–MIT Center for 3D Structure and Physics of the Genome for helpful feedback. Finally, the authors thank L. Mirny for comments on earlier drafts of this paper and for supporting their independent work. This work was supported by NSF 1504942 Physics of Chromosomes (PI: L. Mirny) and U54 DK107980 3D Structure and Physics of the Genome (PIs: J. Dekker and L. Mirny). During revisions, G.F. was supported by the San Simeon Fund (PI: K. Pollard).

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  1. Geoffrey Fudenberg

    Present address: Gladstone Institutes, University of California, San Francisco, California, USA

Authors and Affiliations

  1. Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Geoffrey Fudenberg & Maxim Imakaev

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G.F. and M.I. jointly conceived of the study, performed analyses, and wrote the manuscript, and are listed in alphabetical order on the first page.

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Correspondence to Geoffrey Fudenberg or Maxim Imakaev.

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Fudenberg, G., Imakaev, M. FISH-ing for captured contacts: towards reconciling FISH and 3C. Nat Methods 14, 673–678 (2017). https://doi.org/10.1038/nmeth.4329

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