Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Department of Genetics, University of Georgia, Athens, GA 30602, USA.
Genetics. 2022 Jul 4;221(3). doi: 10.1093/genetics/iyac077.
Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element content than whole flies, but whether this increase in transposable element content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here, we sequenced the genomes of 25 sublines of Drosophila S2 cells and show that transposable element insertions provide abundant markers for the phylogenetic reconstruction of diverse sublines in a model animal cell culture system. DNA copy number evolution across S2 sublines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using transposable element insertions. Analysis of transposable element insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for subline identity.
尽管人们对细胞系基因组在体外随时间发生变化的机制知之甚少，但培养细胞仍被广泛应用于分子生物学领域。先前的研究表明，与完整果蝇相比，培养的果蝇细胞中转座元件含量更高，但这种转座元件含量的增加是由于细胞系建立过程中的初始转座爆发，还是由于细胞培养中的持续转座尚不清楚。在这里，我们对 25 株 Drosophila S2 细胞亚系进行了基因组测序，结果表明，转座元件插入为模型动物细胞培养系统中不同亚系的系统发育重建提供了丰富的标记。S2 亚系的 DNA 拷贝数进化揭示了截然不同的基因组组织模式，这些模式支持使用转座元件插入重建的总体进化历史。转座元件插入位点占据和祖先状态的分析支持一种模型，即在少数逆转座子家族的间歇性活动的主导下发生持续转座。我们的工作表明，在长期的果蝇细胞培养过程中会发生大量的基因组进化，这可能会影响那些不控制亚系身份的实验的可重复性。
