The anatomy and morphology of a plant shoot changes over the course of its development. Although many traits (e.g., leaf size) vary gradually, other traits change abruptly at predictable times in shoot development (Hackett and Murray 1993;Greenwood 1995;Poethig 2003). Two such changes occur during the postembryonic growth of the shoot. The juvenile-to-adult transition (vegetative phase change) occurs early in the life of the shoot, and is marked by differences in the anatomy, morphology, and chemistry of leaves and internodes produced before and after this transition. The second transition (reproductive phase change) occurs during the adult phase, and results in the production of flowers and flower-bearing branches in place of vegetative shoots.

The Arabidopsis genes, TAS2 and TAS1a, produce structurally similar noncoding transcripts that are transformed into short (21-nucleotide [nt]) and long (24-nt) siRNAs by RNA silencing pathways. Some of these short siRNAs direct the cleavage of protein-coding transcripts, and thus function as trans-acting siRNAs (ta-siRNAs). Using genetic analysis, we defined the pathway by which ta-siRNAs and other short siRNAs are generated from these loci. This process is initiated by the miR173-directed cleavage of a primary poly(A) transcript. The 3 fragment is then transformed into short siRNAs by the sequential activity of SGS3, RDR6, and DCL4: SGS3 stabilizes the fragment, RDR6 produces a complementary strand, and DCL4 cleaves the resulting double-stranded molecule into short siRNAs, starting at the end with the miR173 cleavage site and proceeding in 21-nt increments from this point. The 5 cleavage fragment is also processed by this pathway, but less efficiently. The DCL3-dependent pathway that generates long siRNAs does not require miRNA-directed cleavage and plays a minor role in the silencing of these loci. Our results define the core components of a post-transcriptional gene silencing pathway in Arabidopsis and reveal some of the features that direct transcripts to this pathway.[Keywords: PTGS; RNAi; miRNA; trans-acting siRNAs] Supplemental material is available at http://www.genesdev.org.

Mutations in the ARGONAUTE gene ZIPPY(ZIP)/AGO7 in Arabidopsis accelerate the juvenile-to-adult transition. A screen for mutations that suppress this precocious phenotype yielded alleles of two auxin-related transcription factors known to be upregulated in zip: ETTIN (ETT)/ARF3 and ARF4. Mutations in ETT/ARF3 and ARF4 delay the expression of adult traits, demonstrating that these genes have non-redundant roles in shoot maturation. ZIP is not generally required for the production of trans-acting (ta) siRNAs, but is required for the production and/or stability of tasiR-ARF, a ta-siRNA that targets both ETT/ARF3 and ARF4. tasiR-ARF is absent in zip-2, and overexpression of a tasiR-ARF-insensitive form of ETT mimics the zip phenotype. We conclude that the precocious phenotype of zip is attributable to the absence of tasiR-ARF-mediated repression of ETT and ARF4. The abundance of tasiR-ARF, ETT/ARF3 and ARF4 RNA does not change during vegetative development. This result suggests that tasiR-ARF regulation establishes the threshold at which leaves respond to a temporal signal, rather than being a component of this signal.

RNA-induced silencing complexes (RISCs) play central roles in posttranscriptional gene silencing. In plants, the mechanism of RISC assembly has remained elusive due to the lack of cell-free systems that recapitulate the process. In this report, we demonstrate that plant AGO1 protein synthesized by in vitro translation using an extract of evacuolated tobacco protoplasts incorporates synthetic small interfering RNA (siRNA) and microRNA (miRNA) duplexes to form RISCs that sequester the single-stranded siRNA guide strand and miRNA strand, respectively. The formed RISCs were able to recognize and cleave the complementary target RNAs. In this system, the siRNA duplex was incorporated into HSP90-bound AGO1, and subsequent removal of the passenger strand was triggered by ATP hydrolysis by HSP90. Removal of the siRNA passenger strand required the ribonuclease activity of AGO1, while that of the miRNA star strand did not. Based on these results, the mechanism of plant RISC formation is discussed.