Summary Transposable elements represent nearly half of mammalian genomes and are generally described as parasites or ‘junk DNA’. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet is paradoxically highly expressed during early development. Here we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1 and peri-nucleolar chromatin in the regulation of transcription, developmental potency and ES cell self-renewal.

SUMMARY The human naive pluripotent stem cell (PSC) state, corresponding to a pre-implantation stage of development, has been difficult to capture and sustain in vitro. We report that the Hippo pathway effector YAP is nuclearly localized in the inner cell mass of human blastocysts. Overexpression of YAP in human embryonic stem cells (ESCs) and induced PSCs (iPSCs) promotes the generation of naive PSCs. Lysophosphatidic acid (LPA) can partially substitute for YAP to generate transgene-free human naive PSCs. YAP- or LPA-induced naive PSCs have a rapid clonal growth rate, a normal karyotype, the ability to form teratomas, transcriptional similarities to human pre-implantation embryos, reduced heterochromatin levels, and other hallmarks of the naive state. YAP/LPA act in part by suppressing differentiation-inducing effects of GSK3 inhibition. CRISPR/Cas9-generated YAP−/− cells have an impaired ability to form colonies in naive but not primed conditions. These results uncover an unexpected role for YAP in the human naive state, with implications for early human embryology.

Highlights d SINE, L1, and low-complexity repeats barcode genes with distinct functions d Genomic repeats dictate the time and level of gene expression during development d L1-enriched genes are sequestered in the inactive NAD/LAD domains for silencing d L1 RNA promotes the nuclear localization and repression of L1-enriched genes