Two important hallmarks of RNA silencing in plants are (1) its ability to self-amplify by using a mechanism called transitivity and (2) its ability to spread locally and systemically through the entire plant. Crucial advances have been made in recent years in understanding the molecular mechanisms of these phenomena. We review here these recent findings, and we highlight the recently identified endogenous small RNAs that use these advantageous properties to act either as patterning signals in important developmental programs or as a part of regulatory cascades. 1. Introduction RNA silencing is a recently identified mechanism important for the transcriptional and posttranscriptional control of genes and genomes in eukaryotes [1–4]. It also contributes to the defence against viruses [5–10], viroids [11, 12], transposons [13], foreign nucleic acids (e.g., transgenes) [14], and in some cases even against micro-organisms [10, 15, 16]. RNA silencing involves processing of dsRNA by DICERs or DICER-LIKEs to produce small RNA (sRNA) duplexes, capture of the guide siRNA strand by ARGONAUTE (AGO) proteins to form RNA-induced silencing complexes (RISCs) and recognition of homologous target DNA or RNA sequences by RISCs [17–19]. In plants, four endogenous pathways, characterized in Arabidopsis thaliana by four specific DICER-LIKE enzymes (DCLs), are involved in sRNA, that is, small interfering (si)RNA and micro (mi)RNA, production [20] (Figure 1). In the RNA-dependent DNA methylation (RdDM) pathway, DCL3 produces 24nt long siRNAs to establish transcriptional gene silencing [21, 22]. This primary RdDM step is further supported by a secondary sRNA-generating machinery that includes RNA polymerases IV and V, AGO4, RNA-dependent RNA polymerase (RDR)2, chromatin remodelling proteins and DNA, and histone methylases [23]. Figure 1: Posttranscriptional and transcriptional gene silencing pathways. Pri-miRNAs consist of a bulged hairpin flanked by unstructured arms. They are transcribed from the relevant MIR genes and are processed predominantly by the DCL1 “Drosha activity” and further by the DCL1 “Dicer activity,” yielding a miRNA duplex. Before processing, the pri-miRNAs, which can be extremely long, are spliced [ 46]. The DCL1 cofactor, the double-stranded RNA binding protein HYL1, and the 2′-OH ds RNA methyl transferases HEN1, SERRATE, or DAWDLE are not shown [ 34, 47– 51]. Methylation by HEN1serves to protect the miRNA duplex from uridylation and degradation by SDN nucleases [ 52– 57]. With miRNA guide strand and AGO1, a RISC is formed [ 58, 59], which binds to the
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