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A search algorithm to identify active transposable elements in NGS reads

Gabor Hegedus, Katalin Smudla, Viktor Jeles, Dorottya M. Berki.

Statement of the Problem: Transposable Elements (TE, jumping genes, transposons) are highly repetitive DNA segments of various length that can change their positions. Numerous TE exist, but only ~8% of them are transcriptionally active in the human genome (LINE-1, Alu elements) hence encompass the unique capacity to replicate and then insert themselves into different locations within the host DNA. In this way, transposable elements are known to contribute to evolution, genome function and cellular mosaicism, while also underpin several diseases, such as cancer and neurodegenerative disorders, as well as biological aging. Besides their transposition event, their epigenetic regulation has long been recognised as an underlying mechanism for the latter events.