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

by Li, Yun , Boettiger, Alistair , Lee, Lindsay , Wang, Duan Dennis , Ren, Bing , Strambio-De-Castillia, Caterina , Jia, Bojing Blair , Hafner, Antonina , Mishra, Shreya , Jussila, Adam , Yu, Hongyu , Zhu, Chenxu , Xie, Liangqi , Hu, Ming , Chen, Jiawen

in 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

2023

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

2023

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

2023

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Journal Article

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

Li, Yun,

Boettiger, Alistair,

Lee, Lindsay,

Wang, Duan Dennis,

Ren, Bing,

Strambio-De-Castillia, Caterina,

Jia, Bojing Blair,

Hafner, Antonina,

Mishra, Shreya,

Jussila, Adam,

Yu, Hongyu,

Zhu, Chenxu,

Xie, Liangqi,

Hu, Ming,

Chen, Jiawen

2023

Overview

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.

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Publisher

Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

Subject

/ Animals

/ Biology