Current Biology
Volume 21, Issue 22, 22 November 2011, Pages 1888-1893
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The Exoribonuclease Nibbler Controls 3′ End Processing of MicroRNAs in Drosophila

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Summary

MicroRNAs (miRNAs) are endogenous noncoding small RNAs with important roles in many biological pathways; their generation and activity are under precise regulation [1, 2, 3]. Emerging evidence suggests that miRNA pathways are precisely modulated with controls at the level of transcription [4, 5, 6, 7, 8], processing [9, 10, 11], and stability [12, 13], with miRNA deregulation linked with diseases [14] and neurodegenerative disorders [15]. In the Drosophila miRNA biogenesis pathway, long primary miRNA transcripts undergo sequential cleavage [16, 17, 18] to release the embedded miRNAs. Mature miRNAs are then loaded into Argonaute1 (Ago1) within the RNA-induced silencing complex (RISC) [19, 20]. Intriguingly, we found that Drosophila miR-34 displays multiple isoforms that differ at the 3′ end, suggesting a novel biogenesis mechanism involving 3′ end processing. To define the cellular factors responsible, we performed an RNA interference (RNAi) screen and identified a putative 3′→5′ exoribonuclease CG9247/nibbler essential for the generation of the smaller isoforms of miR-34. Nibbler (Nbr) interacts with Ago1 and processes miR-34 within RISC. Deep sequencing analysis revealed a larger set of multi-isoform miRNAs that are controlled by nibbler. These findings suggest that Nbr-mediated 3′ end processing represents a critical step in miRNA maturation that impacts miRNA diversity.

Highlights

► A new fly gene, nibbler/CG9247 (nbr), is identified in miR-34 3′ end processing ► Nbr forms a protein complex with Ago1, and both are required for trimming ► Nbr-mediated 3′ end processing modulates a large number of miRNAs ► Nbr modulation of the miRNA profile impacts gene expression

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These authors contributed equally to this work