SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

Abstract

Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometer and tens of kilobase resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtained comparable results of chromatin loops across datasets generated from diverse imaging technologies.

Spectral-based detection of chromatin loops in multiplexed super-resolution FISH data

“…This results in collections of configurations, sampled with a resolution up to 30 kb, which are for the moment difficult to fully exploit, especially to the aim of loop determination. The most frequent approaches are based on the reconstruction of distance maps, then interpreted as contact maps [23]. However, this approach restricts the information to a level already obtainable with previous techniques.…”