Abstract
Background Close to half of the human genome is derived from transposable elements (TEs), and some TE families continue to generate new insertions through RNA-mediated mechanisms. Due to its mutagenic potential, such retrotransposition is normally suppressed by epigenetic and post-transcriptional mechanisms. However, the epigenetic and regulatory disruptions commonly observed in cancers may allow for TE activation, and a few examples have been reported in lung and colon cancer previously.
Highlights
Close to half of the human genome is derived from transposable elements (TEs), and some TE families continue to generate new insertions through RNA-mediated mechanisms
Materials and methods To systematically evaluate the frequency of such events across different tumor types and assess their impact in human cancers, we developed Tea (Transposable element analyzer), a computational pipeline to detect TE insertions at single nucleotide level and extract their mechanistic signatures
We identified 194 high-confidence somatic TE insertions (183 L1, 10 Alu, 1 ERV), most of which were generated through endonuclease-mediated retrotransposition mechanism
Summary
Eunjung Lee1,2, Rebecca Iskow3, Lixing Yang1, Omer Gokcumen3, Psalm Haseley1,2, Lovelace J Luquette III1, Jens G Lohr4,5, Christopher C Harris6, Li Ding6, Richard K Wilson6, David A Wheeler7, Richard A Gibbs7, Raju Kucherlapati2,8, Charles Lee3, Peter V Kharchenko1, Peter J Park1,2*
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