LINE1 TGS mechanism mediated by SETDB1-AGO2 complex in human somatic cells [small RNA-seq]

LINE1s are abundant retroelements comprising 17% of human genome. Naturally, genomic LINE1s are tightly repressed by epigenetic mechanism; however, if relieved, they can be detrimental to genome stability by their transposition capability. So, a supervising mechanism that quickly re-represses the leaky LINE1s is demanded. Here we show that de-repressed LINE1s generate small RNAs, L1-siRNAs, which SETDB1 and AGO2 recognize, then move into searching for a transcript with sequence complementarity, and ultimately re-install a repression mechanism at LINE1 5’-untranslated region (5’UTR) by depositing trimethyl-H3K9 (H3K9me3). Immunoprecipitation (IP) results showed that SETDB1, AGO2, and L1-siRNA bound to each other and Chromatin-IP-seq and small-RNA-seq results demonstrated that they sat at the same locus within the 5’UTR. SETDB1, AGO2, and L1-siRNA all were necessary for LINE1 repression, particularly the evolutionary young and transposition-competent families such as L1HS/L1PA1 and L1PA2. KAP1, which frequently partners with SETDB1 for silencing local chromatin, was dispensible for the repression of young L1PAs. Our findings indicate that, as a surveillance mechanism, the L1-siRNA-triggered, SETDB1-AGO2-effected repair of epigenetic errors at the 5’UTR establishes a homeostatic re-repression mechanism on inadvertently de-repressed LINE1 copies over the genome. Comparative small RNA expression profiling analysis for HAP1 cells and its SETDB1 KO derivative.