Dicer uses distinct modules for recognizing dsRNA termini

Sinha, Niladri K.; Iwasa, Janet; Shen, Peter; Bass, Brenda

doi:10.1126/science.aaq0921

Cited by 93 publications

(221 citation statements)

References 69 publications

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“…In C. elegans Dicer and Drosophila Dicer2, helicase domain is essential for processing dsRNA with 5′ overhang or blunt ends, but not for dsRNA with 3′ overhangs or canonical pre-miRNAs with 2 nt 3′ overhang ( 40 , 41 ). Because base-pairing interactions could potentially form between the 5′ extension and the 2 nt 3′ overhang, we speculate that Dicer's helicase domain may also contribute to processing a subset of 5′-extended pre-miRNAs.…”

Section: Discussionmentioning

confidence: 99%

Dicer cleaves 5′-extended microRNA precursors originating from RNA polymerase II transcription start sites

Sheng¹,

Fields²,

Aadland

et al. 2018

Nucleic Acids Research

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MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs into the cytoplasm for Dicer processing. Alternatively, pre-miRNAs containing a 5′ 7-methylguanine (m7G-) cap can be generated independently of Drosha and XPO5. Here we identify a class of m7G-capped pre-miRNAs with 5′ extensions up to 39 nt long. The 5′-extended pre-miRNAs are transported by Exportin-1 (XPO1). Unexpectedly, a long 5′ extension does not block Dicer processing. Rather, Dicer directly cleaves 5′-extended pre-miRNAs by recognizing its 3′ end to produce mature 3p miRNA and extended 5p miRNA both in vivo and in vitro. The recognition of 5′-extended pre-miRNAs by the Dicer Platform-PAZ-Connector (PPC) domain can be traced back to ancestral animal Dicers, suggesting that this previously unrecognized Dicer reaction mode is evolutionarily conserved. Our work reveals additional genetic sources for small regulatory RNAs and substantiates Dicer's essential role in RNAi-based gene regulation.

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Section: Discussionmentioning

confidence: 99%

Dicer cleaves 5′-extended microRNA precursors originating from RNA polymerase II transcription start sites

Sheng¹,

Fields²,

Aadland

et al. 2018

Nucleic Acids Research

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show abstract

“…Dicer also contains the helicase domain homologous to those of RLRs (Figure 4a). The structures of human and Drosophila Dicers suggest that the helicase domain can also interact with dsRNA in at least two distinct modes (Figure 4a), one similarly to RLR (155) and the other distinct from RLR (153). The latter was observed in the preslicing conformation.…”

Section: Rna Interference Pathwaymentioning

confidence: 99%

Double-Stranded RNA Sensors and Modulators in Innate Immunity

Hur

2019

Annu. Rev. Immunol.

293

286

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Detection of double-stranded RNAs (dsRNAs) is a central mechanism of innate immune defense in many organisms. We here discuss several families of dsRNA-binding proteins involved in mammalian antiviral innate immunity. These include RIG-I-like receptors, protein kinase R, oligoadenylate synthases, adenosine deaminases acting on RNA, RNA interference systems, and other proteins containing dsRNA-binding domains and helicase domains. Studies suggest that their functions are highly interdependent and that their interdependence could offer keys to understanding the complex regulatory mechanisms for cellular dsRNA homeostasis and antiviral immunity. This review aims to highlight their interconnectivity, as well as their commonalities and differences in their dsRNA recognition mechanisms. KeywordsdsRNA; RIG-I-like receptor; protein kinase R; oligoadenylate synthase; dsRNA-dependent adenosine deaminase; RNA interference HHS Public Access

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“…However, Drosophila melanogaster Dcr-2 appears to have an alternative substrate recognition mode to process viral dsRNA in a PAZ-independent manner, which allows for cleaving dsRNA with a blunt end ( 5 ). This non-conventional substrate recognition is coupled with adenosine triphosphate (ATP) hydrolysis and structural rearrangement of the helicase domain ( 6 ). Upon viral dsRNA recognition and cleavage by Dcr-2, the vsiRNAs are loaded into Argonaute-2 to guide the effector nuclease complex called RISC (RNA Induced Silencing Complex) to target RNAs.…”

Section: Introductionmentioning

confidence: 99%

Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA

Fareh

Lopik

Katechis

et al. 2018

Nucleic Acids Research

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RNA interference (RNAi) is an indispensable mechanism for antiviral defense in insects, including mosquitoes that transmit human diseases. To escape this antiviral defense system, viruses encode suppressors of RNAi that prevent elimination of viral RNAs, and thus ensure efficient virus accumulation. Although the first animal Viral Suppressor of RNAi (VSR) was identified more than a decade ago, the molecular basis of RNAi suppression by these viral proteins remains unclear. Here, we developed a single-molecule fluorescence assay to investigate how VSRs inhibit the recognition of viral RNAs by Dcr-2, a key endoribonuclease enzyme in the RNAi pathway. Using VSRs from three insect RNA viruses (Culex Y virus, Drosophila X virus and Drosophila C virus), we reveal bimodal physical interactions between RNA molecules and VSRs. During initial interactions, these VSRs rapidly discriminate short RNA substrates from long dsRNA. VSRs engage nearly irreversible binding with long dsRNAs, thereby shielding it from recognition by Dcr-2. We propose that the length-dependent switch from rapid screening to irreversible binding reflects the main mechanism by which VSRs distinguish viral dsRNA from cellular RNA species such as microRNAs.

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Dicer uses distinct modules for recognizing dsRNA termini

Cited by 93 publications

References 69 publications

Dicer cleaves 5′-extended microRNA precursors originating from RNA polymerase II transcription start sites

Dicer cleaves 5′-extended microRNA precursors originating from RNA polymerase II transcription start sites

Double-Stranded RNA Sensors and Modulators in Innate Immunity

Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA

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