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DNA copy number evolution in Drosophila cell lines.

Publication ,  Journal Article
Lee, H; McManus, CJ; Cho, D-Y; Eaton, M; Renda, F; Somma, MP; Cherbas, L; May, G; Powell, S; Zhang, D; Zhan, L; Resch, A; Andrews, J ...
Published in: Genome Biol
August 28, 2014

BACKGROUND: Structural rearrangements of the genome resulting in genic imbalance due to copy number change are often deleterious at the organismal level, but are common in immortalized cell lines and tumors, where they may be an advantage to cells. In order to explore the biological consequences of copy number changes in the Drosophila genome, we resequenced the genomes of 19 tissue-culture cell lines and generated RNA-Seq profiles. RESULTS: Our work revealed dramatic duplications and deletions in all cell lines. We found three lines of evidence indicating that copy number changes were due to selection during tissue culture. First, we found that copy numbers correlated to maintain stoichiometric balance in protein complexes and biochemical pathways, consistent with the gene balance hypothesis. Second, while most copy number changes were cell line-specific, we identified some copy number changes shared by many of the independent cell lines. These included dramatic recurrence of increased copy number of the PDGF/VEGF receptor, which is also over-expressed in many cancer cells, and of bantam, an anti-apoptosis miRNA. Third, even when copy number changes seemed distinct between lines, there was strong evidence that they supported a common phenotypic outcome. For example, we found that proto-oncogenes were over-represented in one cell line (S2-DRSC), whereas tumor suppressor genes were under-represented in another (Kc167). CONCLUSION: Our study illustrates how genome structure changes may contribute to selection of cell lines in vitro. This has implications for other cell-level natural selection progressions, including tumorigenesis.

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Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

August 28, 2014

Volume

15

Issue

8

Start / End Page

R70

Location

England

Related Subject Headings

  • Tissue Culture Techniques
  • Sex Chromosomes
  • Sequence Analysis, DNA
  • Selection, Genetic
  • Receptor Protein-Tyrosine Kinases
  • MicroRNAs
  • Male
  • Genetic Variation
  • Genetic Fitness
  • Gene Dosage
 

Citation

APA
Chicago
ICMJE
MLA
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Lee, H., McManus, C. J., Cho, D.-Y., Eaton, M., Renda, F., Somma, M. P., … MacAlpine, D. (2014). DNA copy number evolution in Drosophila cell lines. Genome Biol, 15(8), R70. https://doi.org/10.1186/gb-2014-15-8-r70
Lee, Hangnoh, C Joel McManus, Dong-Yeon Cho, Matthew Eaton, Fioranna Renda, Maria Patrizia Somma, Lucy Cherbas, et al. “DNA copy number evolution in Drosophila cell lines.Genome Biol 15, no. 8 (August 28, 2014): R70. https://doi.org/10.1186/gb-2014-15-8-r70.
Lee H, McManus CJ, Cho D-Y, Eaton M, Renda F, Somma MP, et al. DNA copy number evolution in Drosophila cell lines. Genome Biol. 2014 Aug 28;15(8):R70.
Lee, Hangnoh, et al. “DNA copy number evolution in Drosophila cell lines.Genome Biol, vol. 15, no. 8, Aug. 2014, p. R70. Pubmed, doi:10.1186/gb-2014-15-8-r70.
Lee H, McManus CJ, Cho D-Y, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D. DNA copy number evolution in Drosophila cell lines. Genome Biol. 2014 Aug 28;15(8):R70.

Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

August 28, 2014

Volume

15

Issue

8

Start / End Page

R70

Location

England

Related Subject Headings

  • Tissue Culture Techniques
  • Sex Chromosomes
  • Sequence Analysis, DNA
  • Selection, Genetic
  • Receptor Protein-Tyrosine Kinases
  • MicroRNAs
  • Male
  • Genetic Variation
  • Genetic Fitness
  • Gene Dosage