Expression spectrum of TE-derived transcripts in human adult tissues.

Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the extent to which human TEs drive gene transcription in adult tissues remains largely unexplored. In this study, we systematically analyzed 17,329 human transcriptomes to investigate how TEs influence gene transcription across 47 adult tissues. Our findings reveal that TE-derived transcripts are broadly expressed in human tissues, contributing to both housekeeping functions and tissue-specific gene regulation. We identified sex-specific expression of TE-derived transcripts regulated by sex hormones in breast tissue between females and males. Our results demonstrated that TE-derived alternative transcription initiation significantly enhances the variety of translated protein products, e.g., changes in the N-terminal peptide length of WNT2B caused by TE-derived transcription result in isoform-specific subcellular localization. Additionally, we identified 68 human-specific TE-derived transcripts associated with metabolic processes and environmental adaptation. Together, these findings highlight the pivotal evolutionary role of TEs in shaping the human transcriptome, demonstrating how conserved and human-specific TEs contribute to transcriptional and translational innovation in human genome evolution.