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

Autor: Matthew L Bendall, Miguel de Mulder, Luis Pedro Iñiguez, Aarón Lecanda-Sánchez, Marcos Pérez-Losada, Mario A Ostrowski, R Brad Jones, Lubbertus C F Mulder, Gustavo Reyes-Terán, Keith A Crandall, Christopher E Ormsby, Douglas F Nixon
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Zdroj: PLoS Computational Biology, Vol 15, Iss 9, p e1006453 (2019)
Druh dokumentu: article
ISSN: 1553-734X
1553-7358
DOI: 10.1371/journal.pcbi.1006453
Popis: Characterization of Human Endogenous Retrovirus (HERV) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity. We present Telescope, a computational software tool that provides accurate estimation of transposable 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 the 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 sequencing technology and demonstrates that the retrotranscriptome has potential to be used for cell type identification. We compared our tool with other approaches for quantifying transposable element (TE) expression, and found that Telescope has the greatest resolution, as it estimates expression at specific TE insertions rather 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://github.com/mlbendall/telescope.
Databáze: Directory of Open Access Journals
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