Files
Abstract
Cell culture systems are widely used in molecular biology, yet studies using cultured cells suffer from irreproducible outcomes. One leading cause of irreproducible research comes from the misidentification of cell lines. Genotyping protocols have been established to authenticate human cell lines but are lacking for cell cultures derived from many important model species, including Drosophila melanogaster. Irreproducible research on cell lines could also arise by different mechanisms of genome evolution that are poorly understood, including copy number changes, structural variations, and TE amplification. My work focuses on developing new computational strategies to understand TE dynamics and evolution in the Drosophila cell culture system.
First, I utilized the classical observation that TEs can somatically proliferate in Drosophila cell culture to develop a novel framework that uses genome-wide TE insertion profiles to identify cell line origin and reveals the relationship among different Drosophila cell lines and sub-lines. Using this framework, I found that several Drosophila cell lines (Sg4, mbn2, and OSS_E) were misidentified, and that a subset of LTR retrotransposons is sufficient for cell line authentication. I also developed a short-read-based TE detection approach called ngs_te_mapper2, which provided the first evidence that loss of heterozygosity is a mechanism of shaping genome evolution and TE profiles in Drosophila cell culture.
Next, I used genome-wide TE profiles for multiple S2 sub-lines to understand whether TE amplification in cell culture is due to an initial burst of transposition after cell line establishment or ongoing transposition during routine cell culture. My results provided strong evidence for ongoing transposition model in cell culture and revealed extensive copy number diversity among S2 sub-lines. This work suggests that TE and copy number variations could lead to genomic changes in commonly used cell lines, which may significantly impact functional studies.
Finally, I developed a long-read-based TE detection approach called TELR and applied it to a tetraploid Drosophila cell line called S2R+. My results revealed many TEs that somatically inserted after S2R+ cells became tetraploid. Phylogenomic analysis of in vitro TE insertions also revealed that the TE amplification in cell culture could arise from a single or multiple source lineages.
First, I utilized the classical observation that TEs can somatically proliferate in Drosophila cell culture to develop a novel framework that uses genome-wide TE insertion profiles to identify cell line origin and reveals the relationship among different Drosophila cell lines and sub-lines. Using this framework, I found that several Drosophila cell lines (Sg4, mbn2, and OSS_E) were misidentified, and that a subset of LTR retrotransposons is sufficient for cell line authentication. I also developed a short-read-based TE detection approach called ngs_te_mapper2, which provided the first evidence that loss of heterozygosity is a mechanism of shaping genome evolution and TE profiles in Drosophila cell culture.
Next, I used genome-wide TE profiles for multiple S2 sub-lines to understand whether TE amplification in cell culture is due to an initial burst of transposition after cell line establishment or ongoing transposition during routine cell culture. My results provided strong evidence for ongoing transposition model in cell culture and revealed extensive copy number diversity among S2 sub-lines. This work suggests that TE and copy number variations could lead to genomic changes in commonly used cell lines, which may significantly impact functional studies.
Finally, I developed a long-read-based TE detection approach called TELR and applied it to a tetraploid Drosophila cell line called S2R+. My results revealed many TEs that somatically inserted after S2R+ cells became tetraploid. Phylogenomic analysis of in vitro TE insertions also revealed that the TE amplification in cell culture could arise from a single or multiple source lineages.