The RNA–RNA base pairing potential of human Dicer and Ago2 proteins

Abstract

The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.

Unknown Areas of Activity of Human Ribonuclease Dicer: A Putative Deoxyribonuclease Activity

“…Previously we have shown that hDicer, apart from the canonical substrates, binds structurally diverse short ssRNA molecules [35][36][37][38]. Consequently, we decided to test whether hDcr and its variants lacking the PAZ domain would cleave short ssRNAs.…”

The effect of Dicer knockout on RNA interference using various Dicer substrate interfering RNA structures

“…Previously, shRNA, which has a stem-loop structure, was shown to induce stable and long-lasting gene silencing activity (29)(30)(31). The RNAi gene silencing activity of shRNAs with stem-loop structures requires Dicer activity (23), possibly because the terminal loops of shRNA and pre-miRNAs share similar RNA structures, which interact with the Nterminal helicase domain of Dicer (25,(32)(33)(34). Our results suggest that tetra-loop structures are involved in essential Dicer ribonuclease functions, and may have potential alternative effects through interaction with RNA and protein.…”

Accumulation of AGO2 Facilitates Tumorigenesis of Human Hepatocellular Carcinoma

“…With nuclease and ribonuclease activity [22,23], AGO2 generally affects tumorigenesis by regulating miRNA processing and maturation. Despite AGO2 being an essential mediator of miRNA function, recent studies have also revealed that AGO2 could directly interact with mRNA of famous oncogenes via miRNA-independent ways [20].…”