Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans

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Abstract

In C. elegans, DCR-1 is required for the maturation of both short interfering RNAs (siRNAs) and microRNAs (miRNAs), which are subsequently loaded into different Argonaute proteins to mediate silencing via distinct mechanisms. We used in vivo analyses to show that precursors of small RNAs contain structural features that direct the small RNAs into the RNA interference (RNAi) pathway or the miRNA-processing pathway. Nucleotide changes in the pre-let-7 miRNA precursor that make its stem fully complementary cause the resulting small RNA to be recognized as siRNA and induce binding to RDE-1, which leads to RNAi. Mismatches of 1 to 3 nucleotides at various positions in the stem of the precursor restore direction into the miRNA pathway, as the largest portion of such small RNA variants is associated with ALG-1. The Argonaute proteins to which the small RNAs are bound determine the silencing mode, and no functional overlap between RDE-1 and ALG-1 was detected.

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Figure 1: Characteristics of pre-let-7 and the transgene-derived pre-miRNAs and pre-siRNAs used in this study.
Figure 2: Small RNAs derived from mismatched precursors have an miRNA-like distribution in size fractions and fractionate with HA–ALG-1.
Figure 3: Small RNAs derived from mismatched precursors are bound by ALG-1 rather than RDE-1.
Figure 4: RDE-1 is associated mainly with small RNAs derived from fully matching precursors.

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Acknowledgements

We thank G. Hannon and F. Rivas (Cold Spring Harbor Laboratory) for providing reagents and help with the capture assays, B. Tops (Hubrecht Institute) and C. Mello (University of Massachusetts Medical School) for providing strains and W. Kloosterman for discussions and critical reading of the manuscript. This work was supported by a Vidi fellowship from the Dutch Scientific Organization (NWO) to T.S. and a European Union grant (HPRN-CT-2002-00257) and Netherlands Genomics Initiative grant (050-72-415) to F.A.S.

Author information

F.A.S., S.W.H., K.L.O., K.L.T. and T.S. carried out experiments; T.S., F.A.S., R.F.K. and R.H.A.P. supervised the research; F.A.S. and T.S. wrote the paper.

Correspondence to Florian A Steiner or Titia Sijen.

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