Fig. 1.

Retrotransposons as cis-regulatory elements. a Example of transposable elements functioning as alternative promoters in 2C-like ES cells. Embryonic stem (ES) cells, the pluripotent cells derived from the inner cell mass of the blastocyst, are able to differentiate into all embryo tissues. However, a subpopulation of ES cells can be distinguished for its ability to differentiate into both embryo and extra-embryonic tissues (totipotency). These cells recapitulate the same transcriptional state of totipotent 2 cells, where MERV elements are transcriptionally active and work as alternative promoters for two-cell stage specific genes. b Example of transposable elements functioning as enhancers. ERV and L1 enriched enhancers in cranial neural crest cells (CNCC) affect the expression of genes involved in craniofacial development. Divergent enhancers between human and chimp contribute to species-specific facial phenotypes. The differential activity of these species-biased enhancers also affects intra-human facial variation