Transposable elements have rewired the core regulatory network of human embryonic stem cells

• DOI: 10.1038/ng.600
• Publication Date: 2010-06-06T17:41:50Z
• Authors: Galih Kunarso; Na-Yu Chia; Justin Jeyakani; Catalina Hwang; Xinyi Lu; Yun-Shen Chan; Huck-Hui Ng; Guillaume Bourque
• Keywords: Homeobox protein NANOG; CTCF; Gene regulatory network

Detection of new genomic control elements is critical in understanding transcriptional regulatory networks in their entirety. We studied the genome-wide binding locations of three key regulatory proteins (POU5F1, also known as OCT4; NANOG; and CTCF) in human and mouse embryonic stem cells. In contrast to CTCF, we found that the binding profiles of OCT4 and NANOG are markedly different, with only approximately 5% of the regions being homologously occupied. We show that transposable elements contributed up to 25% of the bound sites in humans and mice and have wired new genes into the core regulatory network of embryonic stem cells. These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells.