HENMT1 restricts endogenous retrovirus activity by methylation of 3’-tRNA fragments

Long terminal repeat (LTR) retroelements such as endogenous retroviruses (ERVs) utilize host tRNA as a primer for reverse transcription, and are thus susceptible to silencing by small RNAs derived from the 3′-end of mature tRNAs (3′-tRFs). Rigorous quantification reveals that tRNA level are not directly proportional to 3’-tRFs but specific isoacceptor and isodecoder sequences are highly enriched in a pattern conserved between mouse and human. We found 3’-tRFs are 2’-O methylated by the small RNA methyltransferase HENMT1 protecting them from degradation and promoting ERV silencing. In the absence of HENMT1, 3’-tRFs are subjected to non-templated tailing by the terminal nucleotidyltransferases TUT4 and TENT2 that regulate small RNA turnover. Due to the perfect sequence complementarity of 3’-tRFs to endogenous retroviral sequences, they have thousands of targets in mammalian genomes. We conducted a massively parallel reporter assay using Mus musculus particle type D , a highly active murine ERV, to determine target site rules for 3’-tRFs. Our results suggest that HENMT1 not only stabilizes germline integrity but also serves transposon control by 3’-tRFs in the soma.