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

Geoff Fudenberg, Maxim Imakaev
doi: https://doi.org/10.1101/081448
Geoff Fudenberg
1Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Maxim Imakaev
1Center for the 3D Structure and Physics of the Genome, and Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Abstract

Deciphering how the one-dimensional information encoded in a genomic sequence is read out in three-dimensions is a pressing contemporary challenge. Chromosome conformation capture (3C) and fluorescence in-situ hybridization (FISH) are two popular technologies that provide important links between genomic sequence and 3D chromosome organization. However, how to integrate views from 3C, or genome-wide Hi-C, and FISH is far from solved. We first discuss what each of these methods measure by reconsidering available matched experimental data for Hi-C and FISH. Using polymer simulations, we then demonstrate that contact frequency is distinct from average spatial distance. We show this distinction can create a seemingly-paradoxical relationship between 3C and FISH. Finally, we consider how the measurement of specific interactions between chromosomal loci might be differentially affected by the two technologies. Together, our results have implications for future attempts to cross-validate and integrate 3C and FISH, as well as for developing models of chromosomes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 17, 2016.
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FISH-ing for captured contacts: towards reconciling FISH and 3C
Geoff Fudenberg, Maxim Imakaev
bioRxiv 081448; doi: https://doi.org/10.1101/081448
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FISH-ing for captured contacts: towards reconciling FISH and 3C
Geoff Fudenberg, Maxim Imakaev
bioRxiv 081448; doi: https://doi.org/10.1101/081448

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