Related Experiment Video
Updated: Jul 19, 2025
09:20
CRISPR-Mediated Reorganization of Chromatin Loop Structure
Published on: September 14, 2018
12.6K
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
Lindsay Lee1, Hongyu Yu2,3, Bojing Blair Jia4,5
1Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
Nature Communications
|August 12, 2023
Summary
A new computational tool, SnapFISH, reliably identifies chromatin loops from multiplexed DNA FISH imaging data in single cells. This method accurately detects known loops and works across different imaging technologies.
Area of Science:
- Genomics
- Molecular Biology
- Cell Biology
Background:
- Multiplexed DNA fluorescence in situ hybridization (FISH) enables high-resolution mapping of chromatin fiber folding in single cells.
- Existing computational methods struggle to reliably identify chromatin loops from complex FISH imaging data.
Purpose of the Study:
- To develop and validate a computational pipeline for accurate chromatin loop identification from multiplexed DNA FISH data.
- To provide a robust tool applicable across diverse imaging technologies.
Main Methods:
- Development of the Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH).
- Processing of multiplexed DNA FISH datasets to identify chromatin loops.
- Validation against known chromatin loops in mouse embryonic stem cells.
Main Results:
- SnapFISH accurately and sensitively identifies known chromatin loops.
- The pipeline demonstrates comparable performance across datasets from various imaging technologies.
- SnapFISH provides a reliable method for analyzing chromatin organization.
Conclusions:
- SnapFISH is a valuable computational tool for analyzing chromatin loops from multiplexed DNA FISH data.
- The tool enhances the study of 3D genome organization at the nanoscale.
- SnapFISH is freely available, promoting accessibility for researchers.
