Active endogenous retroviral elements in human pluripotent stem cells are functional in regulating host gene expression

Human endogenous retroviruses were also called LTR elements which can be bound by transcription factors and marked by different histone modifications. In previous studies, LTR had been considered harmful to genome stability, but recently individual LTR or certain subclasses of LTRs such as LTR7/HERVH and LTR5/HERVK families had been identified as functional elements which had acted as a cis-regulatory element, constructed topological domains and contributed to immunity. However, there were still many LTR elements with unknown functions, and the biological significance of LTR for the host was poorly understood. Overall, our study has not only provided a comprehensive regulatory map of LTRs in human ESCs, but also explored the regulatory models of MER57E3 and LTR5_Hs on host genes. Overall design: RNA-seq of 2 replicates in hESCs and ffEPSCs by targeting LTR5_Hs or ZNF730-MER57E3 in CRISPRi system