Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene–TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.

转座因子（TEs）是一种插入诱变剂，可极大地促进真核基因组的可塑性，影响物种的进化和适应以及个体的生理或疾病。测量TE表达不仅有助于了解TE动员的时间和地点，而且还可以了解此过程如何改变基因表达，染色质可及性或细胞信号传导途径。尽管诸如RNA测序之类的全基因组基因表达测定包括转座子衍生的转录本，但大多数计算分析工具会丢弃或误解TE衍生的读数。新兴方法正在改善对表达的TE基因座的鉴定，并有助于区分允许TE从嵌合基因– TE转录本或普遍转录中动员的TE转录本。