Differential expression of transposable elements in stem cell lineages of the preimplantation embryo

Approximately half of the human genome is comprised of transposable elements (TEs), which are genetic elements capable of amplifying themselves within the genome. Throughout the course of human life, TEs are expressed in germ cells, the preimplantation embryo, and the placenta but silenced elsewhere. However, the functions of TEs during embryonic development are poorly understood. Trophoblast stem (TS), embryonic stem (ES), and extraembryonic endoderm stem (XEN) cells are cell lineages derived from the preimplantation embryo and known to have different TE silencing mechanisms. Thus, it is likely distinct TEs are expressed in each lineage and that proteins coded by these TEs have lineage-specific functions. The purpose of this research was to determine which TEs are expressed in each of these stem cell lineages and to compare expression levels between lineages. Each lineages transcriptome was analyzed by quantifying TE expression in RNA-sequencing data from mouse stem cells. Expression data were then used for differential expression analyses performed between the cell types. It was found that certain families of TEs are distinctly expressed in certain lineages, suggesting expression of these families may be involved in the differentiation and development of each lineage, the understanding of which can lead to improved stem cell therapies and capacity to study human embryonic development.