There are at least three RNA silencing pathways for silencing specific genes in plants. In these pathways, silencing signals can be amplified and transmitted between cells, and may even be self-regulated by feedback mechanisms. Diverse biological roles of these pathways have been established, including defence against viruses, regulation of gene expression and the condensation of chromatin into heterochromatin. We are now in a good position to investigate the full extent of this functional diversity in genetic and epigenetic mechanisms of genome control.

MicroRNAs (miRNAs) are ;21 nucleotide noncoding RNAs produced by Dicer-catalyzed excision from stem-loop precursors. Many plant miRNAs play critical roles in development, nutrient homeostasis, abiotic stress responses, and pathogen responses via interactions with specific target mRNAs. miRNAs are not the only Dicer-derived small RNAs produced by plants: A substantial amount of the total small RNA abundance and an overwhelming amount of small RNA sequence diversity is contributed by distinct classes of 21-to 24-nucleotide short interfering RNAs. This fact, coupled with the rapidly increasing rate of plant small RNA discovery, demands an increased rigor in miRNA annotations. Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature.

ARGONAUTE (AGO) RNA-binding proteins are involved in RNA silencing. They bind to short interfering RNAs (siRNAs) and microRNAs (miRNAs) through a conserved PAZ domain, and, in animals, they assemble into a multisubunit RNA-induced silencing complex (RISC). The mammalian AGO2, termed Slicer, directs siRNA-and miRNA-mediated cleavage of a target RNA. In Arabidopsis, there are 10 members of the AGO family, and the AGO1 protein is potentially the Slicer component in different RNAsilencing pathways. Here, we show that AGO1 selectively recruits certain classes of short silencing-related RNA. AGO1 is physically associated with miRNAs, transacting siRNAs, and transgenederived siRNAs but excludes virus-derived siRNAs and 24-nt siRNAs involved in chromatin silencing. We also show that AGO1 has Slicer activity. It mediates the in vitro cleavage of a mir165 target RNA in a manner that depends on the sequence identity of amino acid residues in the PIWI domain that are predicted by homology with animal Slicer-competent AGO proteins to constitute the RNase catalytic center. However, unlike animals, we find no evidence that AGO1 Slicer is in a high molecular weight RNA-induced silencing complex. The Slicer activity fractionates as a complex of Ϸ150 kDa that likely constitutes the AGO1 protein and associated RNA without any other proteins. Based on sequence similarity, we predict that other Arabidopsis AGOs might have a similar catalytic activity but recruit different subsets of siRNAs or miRNAs.posttranscriptional regulation ͉ ribonuclease ͉ viral RNA ͉ silencing A RGONAUTE (AGO) proteins are implicated in RNAsilencing processes that also involve 21-to 26-nt short RNAs (sRNAs) (1) cleaved from double-stranded or partially doublestranded (ds) RNAs by the RNase III enzyme Dicer. There are several types of RNA-silencing mechanisms, including RNA interference (RNAi), the micro RNA (miRNA) pathway, and RNAdirected chromatin silencing (1). RNAi is a type of RNA silencing in which the Dicer substrate is fully double stranded, the sRNA cleavage product is short interfering RNA (siRNA), and the outcome is targeted destruction of siRNA-complementary RNAs. The miRNA pathway is similar except that the Dicer substrate is an inverted repeat RNA with a partially ds structure, the sRNA is referred to as a miRNA, and the target RNAs can be suppressed at the translational level or degraded as in RNAi, depending on the degree of complementarity between the sRNA and its target. Plants possess an additional class of degradative sRNAs called transacting siRNAs (ta-siRNAs) whose formation depends on the miRNAmediated cleavage of their precursor and its conversion into a dsRNA by RDR6 (2-4). The last pathway, RNA-directed chromatin silencing, is similar to RNAi, but the siRNA targets are either DNA or chromatin-associated RNAs and the outcome is DNA methylation or histone modification at the target locus.In the best understood of these RNA-silencing mechanisms, the duplex siRNAs or miRNAs produced by Dicer are unwound in an ATP-dependent process. One ...

The fission yeast clade, comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus and S. japonicus, occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, suggesting a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.