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; Ming Hu

doi:10.1038/s41467-023-40658-3

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.

Authors

Lindsay Lee¹, Hongyu Yu^{2

3}, Bojing Blair Jia^{4

5}, Adam Jussila⁴, Chenxu Zhu^{6

7

8}, Jiawen Chen⁹, Liangqi Xie^{10

11}, Antonina Hafner¹², Shreya Mishra¹, Duan Dennis Wang¹³, Caterina Strambio-De-Castillia¹⁴, Alistair Boettiger¹², Bing Ren^{6

15}, Yun Li^{16

17

18}, Ming Hu¹⁹

Affiliations

¹ Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
² Department of Statistics, University of Wisconsin Madison, Madison, WI, USA.
³ Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA.
⁴ Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
⁵ Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA.
⁶ Ludwig Institute for Cancer Research, La Jolla, CA, USA.
⁷ New York Genome Center, New York, NY, USA.
⁸ Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
⁹ Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.
¹⁰ Department of Infection Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
¹¹ Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
¹² Department of Developmental Biology, Stanford University, Stanford, CA, USA.
¹³ Chapel Hill High School, Chapel Hill, NC, USA.
¹⁴ Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
¹⁵ Center for Epigenomics & Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
¹⁶ Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA. yunli@med.unc.edu.
¹⁷ Department of Genetics, University of North Carolina, Chapel Hill, NC, USA. yunli@med.unc.edu.
¹⁸ Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA. yunli@med.unc.edu.
¹⁹ Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA. hum@ccf.org.

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 .

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Chromatin* / genetics
DNA* / genetics
In Situ Hybridization, Fluorescence / methods
Mice

Substances

Chromatin
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding