UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology



Document Type


Medical Subject Headings

Animals; Argonaute Proteins; Base Pairing; Base Sequence; Cross-Linking Reagents; Drosophila Proteins; Drosophila melanogaster; Eukaryotic Initiation Factors; Immunoprecipitation; MicroRNAs; Molecular Sequence Data; Protein Binding; RNA; RNA, Messenger; RNA, Small Interfering; RNA-Induced Silencing Complex


Bioinformatics | Computational Biology | Genetics and Genomics | Molecular Biology | Systems Biology


In flies, 22-23-nucleotide (nt) microRNA duplexes typically contain mismatches and begin with uridine, so they bind Argonaute1 (Ago1), whereas 21-nt siRNA duplexes are perfectly paired and begin with cytidine, promoting their loading into Ago2. A subset of Drosophila endogenous siRNAs-the hairpin-derived hp-esiRNAs-are born as mismatched duplexes that often begin with uridine. These would be predicted to load into Ago1, yet accumulate at steady-state bound to Ago2. In vitro, such hp-esiRNA duplexes assemble into Ago1. In vivo, they encounter complementary target mRNAs that trigger their tailing and trimming, causing Ago1-loaded hp-esiRNAs to be degraded. In contrast, Ago2-associated hp-esiRNAs are 2'-O-methyl modified at their 3' ends, protecting them from tailing and trimming. Consequently, the steady-state distribution of esiRNAs reflects not only their initial sorting between Ago1 and Ago2 according to their duplex structure, length, and first nucleotide, but also the targeted destruction of the single-stranded small RNAs after their loading into an Argonaute protein.


Citation: RNA. 2011 Jan;17(1):54-63. doi: 10.1261/rna.2498411. Link to article on publisher's site

Freely available online through the RNA Open Access option.

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at

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