Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

We present Telescope, a computational software tool that provides accurate estimation of transpos able element expression (retrotranscriptome) resolved to specific genomic locations. Telescope directly addresses uncertainty in fragment assignment by reassigning ambiguously mapped fragments to the most probable source transcript as determined within a Bayesian statistical model. We demonstrate th e utility of our approach through single locus analysis of HERV expression in 13 ENCODE cell types. When examined at this resolution, we find that the magnitude and breadth of the retrotranscriptome can be vastly different among cell types. Furthermore, our approach is robust to differences in seque ncing technology, and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying TE expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions r ather than at the TE subfamily level. Telescope performs highly accurate quantification of the retrotranscriptomic landscape in RNA-seq experiments, revealing a differential complexity in the transposable element biology of complex systems not previously observed. Telescope is available at https://g ithub.com/mlbendall/telescope.

Source: PLoS Computational Biology - September 29, 2019 Category: Biology Authors: Matthew L. Bendall Source Type: research