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Computer vision for pattern detection in chromosome contact maps

Author

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  • Cyril Matthey-Doret

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756
    Sorbonne Université, Collège Doctoral)

  • Lyam Baudry

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756
    Sorbonne Université, Collège Doctoral)

  • Axel Breuer

    (ENGIE, Global Energy Management)

  • Rémi Montagne

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

  • Nadège Guiglielmoni

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

  • Vittore Scolari

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

  • Etienne Jean

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

  • Arnaud Campeas

    (ENGIE, Global Energy Management)

  • Philippe Henri Chanut

    (ENGIE, Global Energy Management)

  • Edgar Oriol

    (ENGIE, Global Energy Management)

  • Adrien Méot

    (ENGIE, Global Energy Management)

  • Laurent Politis

    (ENGIE, Global Energy Management)

  • Antoine Vigouroux

    (Institut Pasteur, Synthetic Biology Group)

  • Pierrick Moreau

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

  • Romain Koszul

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

  • Axel Cournac

    (Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, C3BI USR 3756)

Abstract

Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols.

Suggested Citation

  • Cyril Matthey-Doret & Lyam Baudry & Axel Breuer & Rémi Montagne & Nadège Guiglielmoni & Vittore Scolari & Etienne Jean & Arnaud Campeas & Philippe Henri Chanut & Edgar Oriol & Adrien Méot & Laurent Po, 2020. "Computer vision for pattern detection in chromosome contact maps," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19562-7
    DOI: 10.1038/s41467-020-19562-7
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    Cited by:

    1. Jacques Serizay & Cyril Matthey-Doret & Amaury Bignaud & Lyam Baudry & Romain Koszul, 2024. "Orchestrating chromosome conformation capture analysis with Bioconductor," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. Rubén Barcia-Cruz & David Goudenège & Jorge A. Moura de Sousa & Damien Piel & Martial Marbouty & Eduardo P. C. Rocha & Frédérique Roux, 2024. "Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Yanlin Zhang & Mathieu Blanchette, 2022. "Reference panel guided topological structure annotation of Hi-C data," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Olivier Messina & Flavien Raynal & Julian Gurgo & Jean-Bernard Fiche & Vera Pancaldi & Marcelo Nollmann, 2023. "3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Hyelim Jo & Taemook Kim & Yujin Chun & Inkyung Jung & Daeyoup Lee, 2021. "A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    6. Sora Yoon & Aditi Chandra & Golnaz Vahedi, 2022. "Stripenn detects architectural stripes from chromatin conformation data using computer vision," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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