eprintid: 10205416 rev_number: 7 eprint_status: archive userid: 699 dir: disk0/10/20/54/16 datestamp: 2025-03-06 15:20:54 lastmod: 2025-03-06 15:20:54 status_changed: 2025-03-06 15:20:54 type: article metadata_visibility: show sword_depositor: 699 creators_name: Molnar, Janos creators_name: Poti, Adam creators_name: Pipek, Orsolya creators_name: Krzystanek, Marcin creators_name: Kanu, Nnennaya creators_name: Swanton, Charles creators_name: Tusnady, Gabor E creators_name: Szallasi, Zoltan creators_name: Csabai, Istvan creators_name: Szuets, David title: The Genome of the Chicken DT40 Bursal Lymphoma Cell Line ispublished: pub divisions: UCL divisions: B02 divisions: C10 divisions: D19 divisions: G99 keywords: Science & Technology, Life Sciences & Biomedicine, Genetics & Heredity, DT40, gene targeting, tumor suppressor gene, chicken genome, single nucleotide polymorphism, CANCER, GENE, IDENTIFICATION, INTEGRATION, EXPRESSION, SEQUENCE, MUTATION, REPEAT, FORMAT note: Copyright © 2014 Molnar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/ by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. abstract: The chicken DT40 cell line is a widely used model system in the study of multiple cellular processes due to the efficiency of homologous gene targeting. The cell line was derived from a bursal lymphoma induced by avian leukosis virus infection. In this study we characterized the genome of the cell line using whole genome shotgun sequencing and single nucleotide polymorphism array hybridization. The results indicate that wild-type DT40 has a relatively normal karyotype, except for whole chromosome copy number gains, and no karyotype variability within stocks. In a comparison to two domestic chicken genomes and the Gallus gallus reference genome, we found no unique mutational processes shaping the DT40 genome except for a mild increase in insertion and deletion events, particularly deletions at tandem repeats. We mapped coding sequence mutations that are unique to the DT40 genome; mutations inactivating the PIK3R1 and ATRX genes likely contributed to the oncogenic transformation. In addition to a known avian leukosis virus integration in the MYC gene, we detected further integration sites that are likely to de-regulate gene expression. The new findings support the hypothesis that DT40 is a typical transformed cell line with a relatively intact genome; therefore, it is well-suited to the role of a model system for DNA repair and related processes. The sequence data generated by this study, including a searchable de novo genome assembly and annotated lists of mutated genes, will support future research using this cell line. date: 2014-11-01 date_type: published publisher: OXFORD UNIV PRESS INC official_url: https://doi.org/10.1534/g3.114.013482 oa_status: green full_text_type: pub language: eng primo: open primo_central: open_green article_type_text: Article; Journal verified: verified_manual elements_id: 975427 doi: 10.1534/g3.114.013482 medium: Electronic pii: g3.114.013482 lyricists_name: Swanton, Robert lyricists_name: Kanu, Nnennaya lyricists_id: CSWAN79 lyricists_id: NKANU55 actors_name: Kanu, Nnennaya actors_id: NKANU55 actors_role: owner funding_acknowledgements: [Hungarian Academy of Sciences]; [Momentum grant]; K104586 [OTKA]; 12-1-2012-0216 [NFU-KMR]; [Breast Cancer Research Foundation]; [Cancer Research UK]; [Rosetrees Trust]; ID:259303 [EU]; [Prostate Cancer Foundation]; [European Research Council]; [National Institute for Health Research University College London Hospitals Biomedical Research Centre]; 17786 [Cancer Research UK]; 19310 [Cancer Research UK] full_text_status: public publication: G3-GENES GENOMES GENETICS volume: 4 number: 11 pagerange: 2231-2240 pages: 10 event_location: England issn: 2160-1836 citation: Molnar, Janos; Poti, Adam; Pipek, Orsolya; Krzystanek, Marcin; Kanu, Nnennaya; Swanton, Charles; Tusnady, Gabor E; ... Szuets, David; + view all <#> Molnar, Janos; Poti, Adam; Pipek, Orsolya; Krzystanek, Marcin; Kanu, Nnennaya; Swanton, Charles; Tusnady, Gabor E; Szallasi, Zoltan; Csabai, Istvan; Szuets, David; - view fewer <#> (2014) The Genome of the Chicken DT40 Bursal Lymphoma Cell Line. G3-GENES GENOMES GENETICS , 4 (11) pp. 2231-2240. 10.1534/g3.114.013482 <https://doi.org/10.1534/g3.114.013482>. Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10205416/1/Molnar%20et%20al%202014.pdf