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Kronos scRT: a uniform framework for single-cell replication timing analysis

Author

Listed:
  • Stefano Gnan

    (Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université)

  • Joseph M. Josephides

    (Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université)

  • Xia Wu

    (Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université
    Sun Yat-sen University)

  • Manuela Spagnuolo

    (Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université)

  • Dalila Saulebekova

    (Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université)

  • Mylène Bohec

    (Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University)

  • Marie Dumont

    (Institut Curie, PSL Research University, CNRS UMR144, Cell Biology and Cancer)

  • Laura G. Baudrin

    (Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University)

  • Daniele Fachinetti

    (Institut Curie, PSL Research University, CNRS UMR144, Cell Biology and Cancer)

  • Sylvain Baulande

    (Institut Curie, Genomics of Excellence (ICGex) Platform, PSL Research University)

  • Chun-Long Chen

    (Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université)

Abstract

Mammalian genomes are replicated in a cell type-specific order and in coordination with transcription and chromatin organization. Currently, single-cell replication studies require individual processing of sorted cells, yielding a limited number (

Suggested Citation

  • Stefano Gnan & Joseph M. Josephides & Xia Wu & Manuela Spagnuolo & Dalila Saulebekova & Mylène Bohec & Marie Dumont & Laura G. Baudrin & Daniele Fachinetti & Sylvain Baulande & Chun-Long Chen, 2022. "Kronos scRT: a uniform framework for single-cell replication timing analysis," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30043-x
    DOI: 10.1038/s41467-022-30043-x
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    References listed on IDEAS

    as
    1. Vishnu Dileep & David M. Gilbert, 2018. "Single-cell replication profiling to measure stochastic variation in mammalian replication timing," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    2. Stefano Gnan & Ilya M. Flyamer & Kyle N. Klein & Eleonora Castelli & Alexander Rapp & Andreas Maiser & Naiming Chen & Patrick Weber & Elin Enervald & M. Cristina Cardoso & Wendy A. Bickmore & David M., 2021. "Nuclear organisation and replication timing are coupled through RIF1–PP1 interaction," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Benjamin D. Pope & Tyrone Ryba & Vishnu Dileep & Feng Yue & Weisheng Wu & Olgert Denas & Daniel L. Vera & Yanli Wang & R. Scott Hansen & Theresa K. Canfield & Robert E. Thurman & Yong Cheng & Günhan G, 2014. "Topologically associating domains are stable units of replication-timing regulation," Nature, Nature, vol. 515(7527), pages 402-405, November.
    4. Yilong Li & Nicola D. Roberts & Jeremiah A. Wala & Ofer Shapira & Steven E. Schumacher & Kiran Kumar & Ekta Khurana & Sebastian Waszak & Jan O. Korbel & James E. Haber & Marcin Imielinski & Joachim We, 2020. "Patterns of somatic structural variation in human cancer genomes," Nature, Nature, vol. 578(7793), pages 112-121, February.
    5. Takashi Nagano & Yaniv Lubling & Csilla Várnai & Carmel Dudley & Wing Leung & Yael Baran & Netta Mendelson Cohen & Steven Wingett & Peter Fraser & Amos Tanay, 2017. "Cell-cycle dynamics of chromosomal organization at single-cell resolution," Nature, Nature, vol. 547(7661), pages 61-67, July.
    6. Darlan C. Minussi & Michael D. Nicholson & Hanghui Ye & Alexander Davis & Kaile Wang & Toby Baker & Maxime Tarabichi & Emi Sei & Haowei Du & Mashiat Rabbani & Cheng Peng & Min Hu & Shanshan Bai & Yu-w, 2021. "Breast tumours maintain a reservoir of subclonal diversity during expansion," Nature, Nature, vol. 592(7853), pages 302-308, April.
    Full references (including those not matched with items on IDEAS)

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    Cited by:

    1. Dashiell J. Massey & Amnon Koren, 2022. "High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Adam C. Weiner & Marc J. Williams & Hongyu Shi & Ignacio Vázquez-García & Sohrab Salehi & Nicole Rusk & Samuel Aparicio & Sohrab P. Shah & Andrew McPherson, 2024. "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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