Small interfering RNAs (siRNAs) and microRNAs (miRNAs) bind to Argonaute family proteins to form a related set of effector complexes that play diverse roles in post-transcriptional gene regulation throughout the eukaryotic lineage. Here, sequence and structural analysis of the MID domain of the Argonaute proteins identified similarities with a family of allosterically regulated bacterial ligandbinding domains. In vitro and in vivo approaches were used to show that certain Argonaute proteins (those involved in translational repression) have conserved this functional allostery between two distinct sites, one involved in binding miRNA:target duplex and the other in binding the 5' cap feature (m 7 GpppG) of eukaryotic mRNAs. This allostery provides an explanation for how miRNA-bound effector complexes may avoid indiscriminate repressive action (mediated through binding interactions with the cap) prior to full target recognition. KeywordsArgonaute; miRNA; miRNP; m 7 GpppG cap; allostery Small interfering RNAs (siRNAs) and microRNAs (miRNAs) belong to an increasingly broad class of small, non-coding RNA molecules found in diverse organisms 1 . These two groups are broadly distinguished by their biogenesis pathways and their differential loading into distinct Argonaute complexes. siRNAs are generated in the cytoplasm and are loaded into an Argonaute-containing RNA-induced silencing complex (siRISC) to cleave targets with perfect complementarity. miRNAs are transcribed in the nucleus from a specific gene and are ultimately loaded into Argonaute-containing miRNPs (miRISC) that limit the expression of distinct mRNA targets with imperfect complementarity. And, though there are clearly shared molecular features for these two processes (e.g. an Argonaute protein and a small RNA), there are also distinct molecular features and players important both for small RNA loading and target recognition 2 . The Argonaute proteins are composed of several distinct domains with partially understood functions: an N-terminal domain, a PAZ domain that contains the binding site for the 3' end of the small RNA, a MID domain that contains the binding site for the 5' end of the small RNA (which will be the focus of discussion in this manuscript), and the PIWI domain that contains the catalytic center for the cleavage reaction that occurs during RNA interference (Fig. 1a).A number of molecular mechanisms have been proposed to account for the observed posttranscriptional control of miRNA-targeted genes including inhibition of translation initiation or elongation and the promotion of mRNA decay (reviewed in ref. 3). One previous studyCorrespondence should be addressed to R.G. (ragreen@jhmi.edu).. * These authors contributed equally to this work. Author InformationThe authors declare no competing financial interests. NIH Public Access Author ManuscriptNat Struct Mol Biol. Author manuscript; available in PMC 2010 March 8. RESULTS Argonaute MID domain analysis reveals functional groupingsThe mechanistic questions that arose from the studies b...

Background: Argonaute proteins associate with siRNAs and miRNAs to repress gene expression.Results: The N-terminal lobe of Argonaute regulates slicer activity on target mRNAs.Conclusion: RNA binding interactions with the Argonaute proteins determine whether the target mRNA is regulated through slicer-dependent or -independent pathway.Significance: The study provides mechanistic understanding of how Argonaute proteins differentially mediate the RNAi and miRNA-mediated repression pathways.

Discussion on the effect of the anti-proliferative compound, JQ1, and reactivation of latent HIV-1 expression in cell culture systems.