Measuring and interpreting transposable element expression go.nature.com/3epDxrb #Review by @sophie_lanciano and @retrogenomics @ircaninstitute @uca_research @inserm @INSB_CNRS 
Computational tools to analyse RNA-seq data often discard reads derived from transposable elements (TE) but measuring TE expression helps to understand when and where TE mobilization occurs and how it alters gene expression, chromatin accessibility or cellular signalling pathways
Measuring TE expression is not straightforward; not only are TEs highly repeated in their host genome but insertional polymorphisms (presence/absence) and internal sequence polymorphisms between individuals complicate their identification
Moreover, many TE-containing transcripts are not implicated in TE mobilization but rather are gene-TE chimeric transcripts or result from pervasive transcription
The authors review the three challenges faced when assaying TE expression -- 1) their mappability, 2) their variability and 3) the diversity of their transcripts -- and detail the computational and experimental approaches that can help solve these issues
