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Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Author

Listed:
  • Yao-Cheng Lin

    (VIB
    Ghent University)

  • Morgane Boone

    (Unit for Medical Biotechnology, Inflammation Research Center, VIB
    Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University)

  • Leander Meuris

    (Unit for Medical Biotechnology, Inflammation Research Center, VIB
    Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University)

  • Irma Lemmens

    (VIB
    Faculty of Medicine and Health Sciences, Ghent University)

  • Nadine Van Roy

    (Center for Medical Genetics, Ghent University Hospital (MRB))

  • Arne Soete

    (Bioinformatics Core Facility, Inflammation Research Center, VIB)

  • Joke Reumers

    (Laboratory for Translational Genetics
    Vesalius Research Center, VIB)

  • Matthieu Moisse

    (Laboratory for Translational Genetics
    Vesalius Research Center, VIB)

  • Stéphane Plaisance

    (VIB BioInformatics Training and Services (BITS))

  • Radoje Drmanac

    (Complete Genomics Inc.
    BGI-Shenzhen, Building No. 11, Bei Shan Industrial Zone, Yantian District)

  • Jason Chen

    (Complete Genomics Inc.)

  • Frank Speleman

    (Center for Medical Genetics, Ghent University Hospital (MRB))

  • Diether Lambrechts

    (Laboratory for Translational Genetics
    Vesalius Research Center, VIB)

  • Yves Van de Peer

    (VIB
    Ghent University
    Genomics Research Institute, University of Pretoria, Hatfield Campus)

  • Jan Tavernier

    (VIB
    Faculty of Medicine and Health Sciences, Ghent University)

  • Nico Callewaert

    (Unit for Medical Biotechnology, Inflammation Research Center, VIB
    Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University)

Abstract

The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection). Furthermore, we present methods to detect human/vector genome breakpoints and a user-friendly visualization tool for the 293 genome data. We also establish that the genome structure composition is in steady state for most of these cell lines when standard cell culturing conditions are used. This resource enables novel and more informed studies with 293 cells, and we will distribute the sequenced cell lines to this effect.

Suggested Citation

  • Yao-Cheng Lin & Morgane Boone & Leander Meuris & Irma Lemmens & Nadine Van Roy & Arne Soete & Joke Reumers & Matthieu Moisse & Stéphane Plaisance & Radoje Drmanac & Jason Chen & Frank Speleman & Dieth, 2014. "Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms5767
    DOI: 10.1038/ncomms5767
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    Cited by:

    1. Qin Peng & Ziliang Huang & Kun Sun & Yahan Liu & Chi Woo Yoon & Reed E. S. Harrison & Danielle L. Schmitt & Linshan Zhu & Yiqian Wu & Ipek Tasan & Huimin Zhao & Jin Zhang & Sheng Zhong & Shu Chien & Y, 2022. "Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Mathieu Charles & Nicolas Gaiani & Marie-Pierre Sanchez & Mekki Boussaha & Chris Hozé & Didier Boichard & Dominique Rocha & Arnaud Boulling, 2025. "Functional impact of splicing variants in the elaboration of complex traits in cattle," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    3. Zsolt Bodai & Alena L. Bishop & Valentino M. Gantz & Alexis C. Komor, 2022. "Targeting double-strand break indel byproducts with secondary guide RNAs improves Cas9 HDR-mediated genome editing efficiencies," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Amanda R. Krysler & Christopher R. Cromwell & Tommy Tu & Juan Jovel & Basil P. Hubbard, 2022. "Guide RNAs containing universal bases enable Cas9/Cas12a recognition of polymorphic sequences," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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