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

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 ima...

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Published in:Nature communications 2023-08, Vol.14 (1), p.4873-7, Article 4873
Main Authors: Lee, Lindsay, Yu, Hongyu, Jia, Bojing Blair, Jussila, Adam, Zhu, Chenxu, Chen, Jiawen, Xie, Liangqi, Hafner, Antonina, Mishra, Shreya, Wang, Duan Dennis, Strambio-De-Castillia, Caterina, Boettiger, Alistair, Ren, Bing, Li, Yun, Hu, Ming
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Language:English
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45
631/114/2415
631/114/794
631/1647/1513
631/1647/48
631/61/212/177
Animals
Biology
Candidates
Chromatin
Chromatin - genetics
Computer applications
Datasets
Deoxyribonucleic acid
DNA
DNA - genetics
Embryo cells
Fibers
Fluorescence in situ hybridization
Genomes
Humanities and Social Sciences
Imaging
In Situ Hybridization, Fluorescence - methods
Localization
Medical research
Mice
multidisciplinary
Multiplexing
Neighborhoods
Research centers
Science
Science (multidisciplinary)
Stem cells
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cited_by cdi_FETCH-LOGICAL-c541t-d8d47746340f6e85556455179c1ffa0447a71d264bfe05d7fd45577cdbefa7d73
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container_title Nature communications
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creator Lee, Lindsay
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Jia, Bojing Blair
Jussila, Adam
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Wang, Duan Dennis
Strambio-De-Castillia, Caterina
Boettiger, Alistair
Ren, Bing
Li, Yun
Hu, Ming
description 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 . Multiplexed DNA FISH technologies are powerful tools to reveal chromatin spatial organisation. Here, the authors developed SnapFISH, a computational pipeline to identify chromatin loops from multiplexed DNA FISH data.
doi_str_mv 10.1038/s41467-023-40658-3
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subjects 45
631/114/2415
631/114/794
631/1647/1513
631/1647/48
631/61/212/177
Animals
Biology
Candidates
Chromatin
Chromatin - genetics
Computer applications
Datasets
Deoxyribonucleic acid
DNA
DNA - genetics
Embryo cells
Fibers
Fluorescence in situ hybridization
Genomes
Humanities and Social Sciences
Imaging
In Situ Hybridization, Fluorescence - methods
Localization
Medical research
Mice
multidisciplinary
Multiplexing
Neighborhoods
Research centers
Science
Science (multidisciplinary)
Stem cells
title SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
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