Fig. 2.

Working models of TE functions in trans. This figure summarizes the working models of TE-containing functional RNAs. When activated, they may modulate the transcriptome at the transcriptional and posttranscriptional levels. Many of these TE-derived/containing RNA-targeted genes are cell fate regulators and play important roles in development. A LINE2 and inverted complementary LINE2 sequences in the same transcript facilitate the formation of a stable double-stranded RNA structure that serves as premiRNA for generating mature, LINE2-derived microRNAs to regulate LINE2-containing transcripts. B An Alu-containing lncRNA LEADeR is recruited to promoters containing both the Alu sequence and IRF1 binding site. LEADeR interacts with IRF1 and may titrate IRF1 binding to the same promoter through some mechanism, leading to the silencing of differentiation-associated genes. C The interaction between lncRNAs and mRNAs via their complementary Alu sequences may recruit STAU1 to trigger Staufen-mediated mRNA decay. For example, PAX3 and KLF2 mRNAs, which are differentiation inhibitors, will be targeted by Alu-containing lncRNAs to derepress myogenesis and adipogenesis, respectively. D Left panel, A LINE1-containing lncRNA, Fedrr, selectively binds to either the transcriptional activating complex TrxG/MLL or repressive chromatin modulating complex PRC2, and targets repeat-containing promoters via the embedded LINE1 sequence to activate or repress embryonic development-related genes. Right panel, SINEB2-containing SINEUP lncRNAs also serve as scaffolds for translational initiation complexes, including HNRNPK and PTBP1, to increase translation. The SINEB1 sequence within SINEUP is important for increasing translational activity. E ERV-derived Linc-ROR serves as a miR-145 sponge to reduce the quantity of free miR-145 available to target mRNAs encoding the key pluripotent factors SOX2, OCT4 and NANOG to enforce the pluripotency status