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

作者：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 N. Boettiger, Bing Ren, Yun Li, Ming Hu · 发表于：Nature Communications · 年份：2023 · DOI：10.1038/s41467-023-40658-3 · 被引用次数：10 · 研究领域：Genomics and Chromatin Dynamics、Genomic variations and chromosomal abnormalities、Chromosomal and Genetic Variations

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 .