SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
Lee, Lindsay Yu, Hongyu Jia, Bojing Blair Jussila, Adam Zhu, Chenxu Chen, Jiawen Xie, Liangqi Hafner, Antonina Mishra, Shreya Wang, Duan Dennis
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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 .
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Lee L, Yu H, Jia BB, Jussila A, Zhu C, Chen J, Xie L, Hafner A, Mishra S, Wang DD, Strambio-De-Castillia C, Boettiger A, Ren B, Li Y, Hu M. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nat Commun. 2023 Aug 12;14(1):4873. doi: 10.1038/s41467-023-40658-3. PMID: 37573342; PMCID: PMC10423204.
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This article is based on a previously available preprint in bioRxiv, https://doi.org/10.1101/2022.12.16.520793.