Retrotransposon LINE1 trans-inhibiting differentiation maintains embryonic stem cell identity

Long Interspersed Nuclear Elements-1s (LINE1s) are one of the >17% most abundant Retrotransposons in mammalian genomes. LINE1 RNA is high expression during early embryonic development, meanwhile is under tight epigenetic control. Some studies have confirmed LINE1 play a critical role in early embryo development and ESC identity. Previous studies focused on the role of LINE1 in cis-regulation, however, the function of L1 RNA in tans-regulation remains largely unknown. In this study, we performed a high-throughput proximity MARGI (pxMARGI) experiment found transposon LINE1 RNA trans-regulated prefer to young LINE1 subfamily, and in hybrid and non-hybrid two different manner repress ESC to dual progress of 2C-like cells and differentiation. In differentiation process, LINE1 RNA as a scaffold recruit polycomb core subunits combine three core pluripotent factors maintain ESC identity. In 2C process, LINE1 RNA in a sequence-specific manner recruit Kap1 to old L1 subfamily, and recruit ELL3 to RE 5‘UTR maintain ESC self-renewal. Our data point to LINE1 transcriptions more detail trans-regulation mechanism to orchestrate developmental progression for the self-renewal of embryonic stem cells (ESCs). LINE1 RNA may be potential biomarker for noninvasive embryo selection.