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

Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Shreya Mishra, Duan Dennis Wang, Caterina Strambio- De-Castillia, Alistair Boettiger, Bing Ren, Yun Li () and Ming Hu ()
Additional contact information
Lindsay Lee: Cleveland Clinic Foundation
Hongyu Yu: University of Wisconsin Madison
Bojing Blair Jia: University of California San Diego
Adam Jussila: University of California San Diego
Chenxu Zhu: Ludwig Institute for Cancer Research
Jiawen Chen: University of North Carolina
Liangqi Xie: Lerner Research Institute, Cleveland Clinic Foundation
Antonina Hafner: Stanford University
Shreya Mishra: Cleveland Clinic Foundation
Duan Dennis Wang: Chapel Hill High School
Caterina Strambio- De-Castillia: University of Massachusetts Chan Medical School
Alistair Boettiger: Stanford University
Bing Ren: Ludwig Institute for Cancer Research
Yun Li: University of North Carolina
Ming Hu: Cleveland Clinic Foundation

Nature Communications, 2023, vol. 14, issue 1, 1-7

Abstract: Abstract Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in 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 obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .

Date: 2023
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DOI: 10.1038/s41467-023-40658-3

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