You'd Prefer An Argonaute

RNA Journal Club 11/11/10

Posted in RNA Journal Club, RNAJC w/ review by YPAA on December 13, 2010

Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis

Josh T Cuperus, Alberto Carbonell, Noah Fahlgren, Hernan Garcia-Ruiz, Russell T Burke, Atsushi Takeda, Christopher M Sullivan, Sunny D Gilbert, Taiowa A Montgomery & James C Carrington

Nature Structural & Molecular Biology Volume 17, Number 8, 997–1003, August 2010.
DOI: doi:10.1038/nsmb.1866

This week’s fluid summary and analysis by Vikram Agarwal:

Over the past half-decade, one of the questions that has persisted in field of plant small RNA biology is that of how 21-nt short interfering RNAs (siRNAs) emerge from transcripts that are targeted by microRNAs (miRNAs).  Only a few aspects of the pathway have been characterized: first, an Argonaute-miRNA complex recognizes its target and cleaves it; second, RDR6, and RNA-dependent RNA polymerase, is recruited to synthesize an antisense transcript using the cleaved transcript as a template; and finally, Dicer-like 1 (DCL1) recognizes the double stranded RNA and processively cleaves it into phased 21-nt RNAs, which are presumably loaded into new Argonautes to cleave new targets.  These siRNAs are assumed to predominantly act in cis, serving as a positive feedback mechanism to rapidly degrade the original miRNA target.  However, several that emerge from the noncoding TAS genes after miRNA-mediated cleavage are known to act in trans, guiding the downstream targeting of genes that coordinate the response to auxin, a phytohormone that is critical for proper plant growth and development.

Yet another observation that has been difficult to explain is why only a handful of miRNA-targeted transcripts produce these siRNAs, whereas the vast majority apparently do not recruit RDR6 and produce siRNAs.  In this article, Cuperus and colleagues seek to address these questions; they demonstrate that a common feature of most RDR6-dependent siRNA generating transcripts is their targeting by 22-nt miRNAs, and that this targeting is sufficient for the production of siRNAs.  They begin their study by exploring the distribution of small RNA size classes that arise from transcripts that are either targeted or not targeted by miRNAs.  As expected, they find targeted transcripts predominantly produce phased, 21-nt small RNAs, the signature of DCL1-mediated cleavage (Figure 1a,b).  Most importantly, they find that 21-nt-generating loci are overwhelmingly targeted by 22-nt small RNAs (Figure 1d).  This sharp asymmetry sets the stage for characterizing the biogenesis and role of 22-nt miRNAs.

Mining published small RNA sequencing libraries, they identify precursor loci that produce a mature miRNA primarily in the 21-nt or 22-nt species, both in Arabidopsis and rice (Figure 2b).  Probing for any structural biases in the precursors that give rise to 22-nt miRNAs, they find that most contain an asymmetric bulge in the miRNA-miRNA* pairing interface, though this is not an absolute requirement (Figure 2c,d).  Exploiting this knowledge, they construct artificial miRNAs (amiRNAs) of miR173 that contain a symmetric or asymmetric bulge, generating mature 21 and 22-nt mature miRNA species, respectively (Figure 3a,b).  Interestingly, only the 22-nt natural miRNA and 22-nt amiRNA, but not the 21-nt amiRNA, successfully guide phased siRNA production (Figure 3b,c), though all miRNAs are successfully loaded into Ago1 and cleave their targets (Figure 3d-f).  Moreover, these observations are not specific to miR173, but hold true for amiRNA constructs comparing 21 and 22-nt variants of miR473 and miR828 (Figure 4a-d).

Collectively, these results suggest a general mechanism –22-nt miRNAs are the key determinants that guide the subsequent synthesis of phased siRNAs.  Overall, this paper provides an explanation for a long-observed phenomenon.  However, the reader is left wondering about the underlying molecular mechanism: how can the seemingly innocuous addition of a single base on a mature miRNA recruit RDR6 and thereby orchestrate a completely novel molecular trajectory?  Why is it that there are still targets that produce siRNAs but are not targeted by a 22-nt miRNA, and conversely, why are there targets of 22-nt miRNAs that do not produce detectable secondary siRNAs?  Clearly, the proposed model does not cover all bases, and there is still much to be learned about the missing players in this pathway.

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