The architectural and functional landscape of transposon-derived chimeric RNAs.

This review systematically examines the architectural and functional landscape of transposable element (TE)-derived chimeric RNAs, classifying them into three major categories: TE-coding gene chimeras, TE-lncRNA chimeras and TE-TE chimeras. We delineate four potential molecular mechanisms contributing to their biogenesis: transcriptional read-through coupled with cis-splicing, promoter hijacking by TE-derived regulatory elements, trans-splicing of independent transcripts and epigenetic regulation of TE genomic loci. Functionally, TE and their chimeric RNAs can coordinately participate in genomic regulation at different levels: they remodel native gene expression patterns via alternative promoters, introduce novel functional domains into proteins and lncRNAs, and form integrated transcriptional regulatory networks. These chimeric transcripts exert critical roles in early embryonic development, stem cell potency, differentiation or pathogenic condition. Looking forward, long-read sequencing and genomic targeting technologies hold great promise to unravel the functionality and therapeutic application of TE-derived chimeric RNAs. Collectively, this review establishes TE-derived chimeric RNAs as fundamental drivers of transcriptomic innovation, evolutionary adaptation and disease aetiology, bridging basic genome biology with physiology and clinical translation.