Human tRNA-derived small RNAs in the global regulation of RNA silencing

Abstract

Competition between mammalian RNAi-related gene silencing pathways is well documented. It is therefore important to identify all classes of small RNAs to determine their relationship with RNAi and how they affect each other functionally. Here, we identify two types of 59-phosphate, 39-hydroxylated human tRNA-derived small RNAs (tsRNAs). tsRNAs differ from microRNAs in being essentially restricted to the cytoplasm and in associating with Argonaute proteins, but not MOV10. The first type belongs to a previously predicted Dicer-dependent class of small RNAs that we find can modestly down-regulate target genes in trans. The 59 end of type II tsRNA was generated by RNaseZ cleavage downstream from a tRNA gene, while the 39 end resulted from transcription termination by RNA polymerase III. Consistent with their preferential association with the nonslicing Argonautes 3 and 4, canonical gene silencing activity was not observed for type II tsRNAs. The addition, however, of an oligonucleotide that was sense to the reporter gene, but antisense to an overexpressed version of the type II tsRNA, triggered robust, >80% gene silencing. This correlated with the redirection of the thus reconstituted fully duplexed double-stranded RNA into Argonaute 2, whereas Argonautes 3 and 4 were skewed toward less structured small RNAs, particularly single-strand RNAs. We observed that the modulation of tsRNA levels had minor effects on the abundance of microRNAs, but more pronounced changes in the silencing activities of both microRNAs and siRNAs. These findings support that tsRNAs are involved in the global control of small RNA silencing through differential Argonaute association, suggesting that small RNA-mediated gene regulation may be even more finely regulated than previously realized.

Circulating microRNA signature of genotype‐by‐age interactions in the long‐lived Ames dwarf mouse

“…These new small RNAs are being noticed only now because most studies focused on sequencing reads derived from miRNAs. Accumulating evidence suggests that these RNA fragments are functional in physiological and pathological conditions (Rutjes et al ., 1999; Haussecker et al ., 2010; Anderson & Ivanov, 2014). In particular, tRNA halves have been described in the cytoplasm of stressed cultured cells where they have been reported to function in key biological processes, that is, translation and apoptosis (Ivanov et al ., 2011; Anderson & Ivanov, 2014) and may be involved in human diseases including cancer, neurodegeneration, and infection [reviewed in Anderson & Ivanov (2014)].…”

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…Interestingly, recent studies report that these elements may contribute to gene regulation, being cleaved by DICER RNAse to produce stable RNA products rather than being just randomly generated degradation products (Haussecker et al 2010;Cole et al 2009;Sobala and Hutvagner 2011).…”

RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage

“…Defined tRNA fragments have been identified through small RNA cloning approaches (Kawaji et al 2008;Cole et al 2009;Haussecker et al 2010), suggesting a physiological role for tRNA fragments. Interestingly, tRNA fragments can be processed to smaller RNAs by the Dicer RNase, indicating a potential interaction of tRNA-derived sequences and canonical small RNA processing pathways (Cole et al 2009).…”

“…Interestingly, tRNA fragments can be processed to smaller RNAs by the Dicer RNase, indicating a potential interaction of tRNA-derived sequences and canonical small RNA processing pathways (Cole et al 2009). Indeed, a recent study provided evidence that tRNA-derived small RNAs act to down-regulate target mRNAs, and affect different RNA silencing pathways by associating with effector core components (Haussecker et al 2010). This suggests that altered tRNA cleavage (e.g., under stress conditions) could have phenotypic consequences.…”