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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. Electronic supplementary material The online version of this article (10.1007/s00018-019-03344-6) contains supplementary material, which is available to authorized users.

Rybonukleaza Dicer jest znana przede wszystkim z kluczowej roli, jaką odgrywa w proce­sie biogenezy krótkich regulatorowych RNA: miRNA oraz siRNA. Badania prowadzone w ostatnich latach znacząco wzbogaciły wiedzę dotyczącą funkcji pełnionych przez Dicer. Wykazano, że Dicer jest zaangażowana w metabolizm zróżnicowanej puli RNA, m.in. tRNA i snoRNA, usuwanie potencjalnie cytotoksycznych cząsteczek RNA oraz utrzymywanie sta­bilności genomu. Co więcej, podczas apoptozy, w następstwie cięcia proteolitycznego przez kaspazy, fragment Dicer staje się deoksyrybonukleazą i bierze udział w degradacji genomo­wego DNA. Odkrycie mechanizmu pasywnego wiązania RNA przez Dicer oraz jej aktywno­ści opiekuńczych wobec kwasów nukleinowych wykazało, że Dicer może dodatkowo pełnić funkcje niezwiązane z hydrolizą kwasów nukleinowych. W tym artykule podsumowujemy aktualny stan wiedzy na temat struktury i funkcjonowania ludzkiej rybonukleazy Dicer, uwzględniając kanoniczną rolę enzymu w biogenezie miRNA oraz nowo odkrywane obsza­ry jej aktywności.

Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.

Guanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform–PAZ–Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation. Supplementary Information The online version contains supplementary material available at 10.1007/s00018-021-03795-w.