Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells [RNA-seq]

Transposable elements (TEs) appear to have contributed to the evolution of tissue-specific gene regulatory networks in contexts such as early development, pregnancy and innate immunity, amongst others. In mouse embryonic stem cells (ESCs), TE families such as RLTR13D6 bind key pluripotency-associated transcription factors and are enriched for histone marks that are characteristic of distal enhancers. However, it remains unclear to what extent such lineage-specific TEs are important for maintaining gene expression programmes during preimplantation development. Here we have tested the gene regulatory function of RLTR13D6 elements in ESCs using epigenetic editing approaches. Whilst we identify some elements that are important to drive gene expression, these constitute a minority of all the putative TE-derived enhancers identified through epigenomic analyses, highlighting the importance of functional tests when assessing the contribution of TEs to gene regulatory networks. Overall design: RLTR13D6 elements were silenced in mouse ESCs by CRISPRi with two sets of 4 sgRNAs each, using the empty sgRNA vector as a control. H3K27ac ChIP-seq and RNA-seq libraries were generated.