HERVHLin modulates pluripotency and protects the genome from active retroelements by rewiring the conserved LIN28A/let-7 pathway

Sequential waves of coding transcript expression mark genome reactivation during embryonic development and reprogramming to pluripotency. We additionally observed two distinct waves of non-coding retrotransposable element (RE) expression: an initial wave of younger, partially active REs (LINE-1, SVA, and Alu), followed by older HERVH elements. These waves are not merely correlative, as HERVH depletion leads to an increase in transposition of L1, Alu, and SVA elements. We identified a great apes-specific subgroup of HERVH (N=101), termed HERVHLin, characterized by a motif with duplicated LIN28 binding sites, which alone inhibits L1 transposition. HERVHLin transcripts bind to LIN28 and allow let-7 microRNA to mature, rewiring the conserved LIN28-let-7 regulatory axis. Full locus HERVHLin knockout (KO) results in increased LINE-1 transposition, rescued by the let-7 mimic. HERVHLin KO presents an EMT-like phenotype, downregulation of RE-defense and pluripotency-specific genes, underscoring the role of HERVHLin in genome protection of pluripotent stem cells. HERVHlin chrX knock-out clone (chrX-KO_H1) and control clone (chrX-ctrl_H1) were cultured for 5 or 4 sequential passages (respectively), which were treated like technical replicates, collected for RNA isolation and total RNA sequencing with rRNA depletion was performed. Differentially expressed genes between chrX-ctrl_H1 and chrX-KO_H1 were analysed