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iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Author

Listed:
  • Eleni Gelali

    (Karolinska Institutet)

  • Gabriele Girelli

    (Karolinska Institutet)

  • Masahiro Matsumoto

    (Medical Business Group, Sony Imaging Products & Solutions, Inc.)

  • Erik Wernersson

    (Karolinska Institutet)

  • Joaquin Custodio

    (Karolinska Institutet)

  • Ana Mota

    (Karolinska Institutet)

  • Maud Schweitzer

    (Karolinska Institutet)

  • Katalin Ferenc

    (Karolinska Institutet)

  • Xinge Li

    (Karolinska Institutet)

  • Reza Mirzazadeh

    (Karolinska Institutet)

  • Federico Agostini

    (Karolinska Institutet)

  • John P. Schell

    (Karolinska Institutet
    Stockholm node, Karolinska Institutet
    Karolinska Universitetssjukhuset)

  • Fredrik Lanner

    (Karolinska Institutet
    Stockholm node, Karolinska Institutet
    Karolinska Universitetssjukhuset)

  • Nicola Crosetto

    (Karolinska Institutet)

  • Magda Bienko

    (Karolinska Institutet)

Abstract

DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.

Suggested Citation

  • Eleni Gelali & Gabriele Girelli & Masahiro Matsumoto & Erik Wernersson & Joaquin Custodio & Ana Mota & Maud Schweitzer & Katalin Ferenc & Xinge Li & Reza Mirzazadeh & Federico Agostini & John P. Schel, 2019. "iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09616-w
    DOI: 10.1038/s41467-019-09616-w
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    Cited by:

    1. Jinxin Phaedo Chen & Constantin Diekmann & Honggui Wu & Chong Chen & Giulia Chiara & Enrico Berrino & Konstantinos L. Georgiadis & Britta A. M. Bouwman & Mohit Virdi & Luuk Harbers & Sara Erika Bellom, 2024. "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Ana Mota & Szymon Berezicki & Erik Wernersson & Luuk Harbers & Xiaoze Li-Wang & Katarina Gradin & Christiane Peuckert & Nicola Crosetto & Magda Bienko, 2022. "FRET-FISH probes chromatin compaction at individual genomic loci in single cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Robin Aguilar & Conor K. Camplisson & Qiaoyi Lin & Karen H. Miga & William S. Noble & Brian J. Beliveau, 2024. "Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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