Abstract
Recent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented detail. However, several cellular aspects are currently underutilized in single cell studies. One aspect is the expression and activity of transposable elements (TEs). TEs are selfish sequences of DNA that can replicate, and have been wildly successful in colonizing genomes. However, most TEs are mutated, fragmentary and incapable of transposition, yet they are actively bound by multiple transcription factors, host complex patterns of chromatin modifications, and are expressed in mRNAs as part of the transcriptome in both normal and diseased states. The contribution of TEs to development and cellular function remains unclear, and the routine inclusion of TEs in single cell sequencing analyses will potentially lead to insight into stem cells, development and human disease.
Highlights
transposable elements (TEs) are self-replicating sequences of DNA that have colonized nearly 50% of typical mammalian genomes, and take up more DNA sequence than the exons of coding genes
TEs that successfully duplicate during embryogenesis or in the germ cells can potentially enter the generation
TEs are active during embryogenesis
Summary
TEs are self-replicating sequences of DNA that have colonized nearly 50% of typical mammalian genomes, and take up more DNA sequence than the exons of coding genes. The LINE L1 family is active in humans, and during embryogenesis several TE duplications are potentially introduced into single cells of the germ line, resulting in mosaic germ cells with novel TE insertions (Faulkner and Billon 2018). Innovations in spatial single cell RNA/DNA-seq, which preserves the location of a cell in its tissue, coupled to sequencing of novel retrotransposition events, could lead to a detailed developmental roadmap of the human brain.
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