TY - JOUR N1 - 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. KW - Science & Technology KW - Life Sciences & Biomedicine KW - Genetics & Heredity KW - DT40 KW - gene targeting KW - tumor suppressor gene KW - chicken genome KW - single nucleotide polymorphism KW - CANCER KW - GENE KW - IDENTIFICATION KW - INTEGRATION KW - EXPRESSION KW - SEQUENCE KW - MUTATION KW - REPEAT KW - FORMAT AV - public TI - The Genome of the Chicken DT40 Bursal Lymphoma Cell Line SN - 2160-1836 EP - 2240 IS - 11 SP - 2231 VL - 4 PB - OXFORD UNIV PRESS INC JF - G3-GENES GENOMES GENETICS A1 - Molnar, Janos A1 - Poti, Adam A1 - Pipek, Orsolya A1 - Krzystanek, Marcin A1 - Kanu, Nnennaya A1 - Swanton, Charles A1 - Tusnady, Gabor E A1 - Szallasi, Zoltan A1 - Csabai, Istvan A1 - Szuets, David Y1 - 2014/11/01/ UR - https://doi.org/10.1534/g3.114.013482 ID - discovery10205416 N2 - 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. ER -