Manganese-dependent microRNA trimming by 3′→5′ exonucleases generates 14-nucleotide or shorter tiny RNAs

MicroRNAs (miRNAs) are about 22-nucleotide (nt) noncoding RNAs forming the effector complexes with Argonaute (AGO) proteins to repress gene expression. Although tiny RNAs (tyRNAs) shorter than 19 nt have been found to bind to plant and vertebrate AGOs, their biogenesis remains a long-standing question. Here, our in vivo and in vitro studies show several 3 '-> 5 ' exonucleases, such as interferon-stimulated gene 20 kDa (ISG20), three prime repair exonuclease 1 (TREX1), and ERI1 (enhanced RNAi, also known as 3 ' hExo), capable of trimming AGO-associated full-length miRNAs to 14-nt or shorter tyRNAs. Their guide trimming occurs in a manganese-dependent manner but independently of the guide sequence and the loaded four human AGO paralogs. We also show that ISG20-mediated guide trimming makes Argonaute3 (AGO3) a slicer. Given the high Mn2+ concentrations in stressed cells, virus-infected cells, and neurode-generation, our study sheds light on the roles of the Mn2+-dependent exonucleases in remodeling gene silencing.

Automated summary

MicroRNAs (miRNAs), a type of noncoding RNA with about 22 nucleotides, can form complexes with Argonaute (AGO) proteins to repress gene expression. This study discovered that certain exonucleases, including ISG20, TREX1, and ERI1, are capable of trimming AGO-associated full-length miRNAs to shorter tyRNAs in a manganese-dependent manner. The study also showed that ISG20-mediated trimming converts AGO3 into a slicer. These findings shed light on the roles of manganese-dependent exonucleases in gene silencing.