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To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.10.040 Byline: J. Graham Ruby (1)(2), Calvin Jan (1)(2), Christopher Player (1), Michael J. Axtell (1), William Lee (3), Chad Nusbaum (3), Hui Ge (1), David P. Bartel (1)(2) Abstract: We sequenced [approximately equal to]400,000 small RNAs from Caenorhabditis elegans. Another 18 microRNA (miRNA) genes were identified, thereby extending to 112 our tally of confidently identified miRNA genes in C. elegans. Also observed were thousands of endogenous siRNAs generated by RNA-directed RNA polymerases acting preferentially on transcripts associated with spermatogenesis and transposons. In addition, a third class of nematode small RNAs, called 21U-RNAs, was discovered. 21U-RNAs are precisely 21 nucleotides long, begin with a uridine 5'-monophosphate but are diverse in their remaining 20 nucleotides, and appear modified at their 3'-terminal ribose. 21U-RNAs originate from more than 5700 genomic loci dispersed in two broad regions of chromosome IV -- primarily between protein-coding genes or within their introns. These loci share a large upstream motif that enables accurate prediction of additional 21U-RNAs. The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs). Author Affiliation: (1) Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA (2) Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA (3) Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Article History: Received 16 June 2006; Revised 23 September 2006; Accepted 27 October 2006 Article Note: (miscellaneous) Published: December 14, 2006

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.09.032 Byline: Michael J. Axtell (1)(2), Calvin Jan (1)(2), Ramya Rajagopalan (1)(2), David P. Bartel (1)(2) Abstract: In Arabidopsis, microRNA-directed cleavage can define one end of RNAs that then generate phased siRNAs. However, most miRNA-targeted RNAs do not spawn siRNAs, suggesting the existence of additional determinants within those that do. We find that in moss, phased siRNAs arise from regions flanked by dual miR390 cleavage sites. AtTAS3, an siRNA locus important for development and conserved among higher plants, also has dual miR390 complementary sites. Both sites bind miR390 in vitro and are functionally required in Arabidopsis, but cleavage is undetectable at the 5' site -- demonstrating that noncleavable sites can be functional in plants. Phased siRNAs also emanate from the bounded regions of every Arabidopsis gene with two known microRNA/siRNA complementary sites, but only rarely from genes with single sites. Therefore, two 'hits,' -- often, but not always, two cleavage events -- constitute a conserved trigger for siRNA biogenesis, a finding with implications for recognition and silencing of aberrant RNA. Author Affiliation: (1) Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA (2) Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA Article History: Received 21 March 2006; Revised 7 July 2006; Accepted 25 September 2006 Article Note: (miscellaneous) Published: November 2, 2006

Results support a model of plant innate immune recognition. The Arabidopsis-Pseudomonas syringae model shows that NB-LBR proteins initiate signaling process due to hostile modifications to host proteins caused by pathogen-derived molecules. Data suggest that RPS2 protein in Arabidopsis initiates signaling on the disappearance of RIN4 rather than direct recognition of the bacterial effector protein AvrRpt2.