Fig. 1

TEs and single cells, strategies to understand and exploit their properties. a Inactive TEs in the genome can be expressed as mRNAs. They can take several forms: as unspliced individual TE units, spliced TEs, as part of spliced or unspliced noncoding transcripts, or as part of coding transcripts, as unique promoters or inside UTRs (untranslated regions). b TEs are expressed in a cell type-specific manner, and can be markers for cell type specification. Shown is a schematic of the situation in a mouse PSC culture. Most cells are pluripotent, and express various ERVKs, a small number of cells express MERVL and have some totipotent properties, whilst some cells express IAPs, which may be associated with reduced developmental potency. c TE transposition to infer developmental lineages. Transposition of TEs can act as natural ‘barcodes’ to track the developmental lineage of adult human cells. As somatic variation is introduced during development it is propagated during subsequent cell divisions. Ultimately the pattern of TE insertions could be sequenced in single cells, and coupled with spatial transcriptomics could generate a detailed developmental roadmap for human tissues, where genetic engineering of artificial barcode systems is unavailable. d TEs harbor transcription factor binding sites, and recruit specific transcription factors and chromatin modifiers to modify the epigenetic state at TEs. These examples are taken from binding patterns observed in mouse PSCs