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

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 polyme

SUBMITTER: Fudenberg G 

PROVIDER: S-EPMC5517086 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature