![]() 1993) (see sidebar Three Major Types of Small RNAs). ![]() elegans identified the first endogenous small RNA, now known as microRNA (miRNA) ( Lee et al. As early as 1993, long before the mechanism of RNA silencing was uncovered, elegant molecular genetic studies in C. Small RNAs are not derived only from transgenes. Transcripts from the transgenes are converted into dsRNAs, which are processed into small interfering RNAs (siRNAs) (see sidebar Three Major Types of Small RNAs) that guide the cleavage of homologous RNAs to lead to gene silencing. The previously observed transgene-mediated silencing phenomena against viruses and endogenous genes are now understood to be manifestations of RNA silencing. These and biochemical studies performed in animals demonstrated that small RNAs, which are produced from long dsRNAs, guide the cleavage of complementary target mRNAs in RNA silencing (reviewed in Hannon 2002). Another breakthrough study, by Hamilton & Baulcombe, uncovered small RNAs derived from plant transgenes undergoing RNA silencing ( Hamilton & Baulcombe 1999). A breakthrough study by Fire and colleagues in Caenorhabditis elegans revealed that long double-stranded RNAs (dsRNAs) confer effective sequence-specific silencing of endogenous genes in a process named RNA interference or RNA silencing ( Fire et al. The transgene-mediated gene silencing or viral protection exhibited sequence specificity, but the underlying mechanism was unknown. It was also found that transgenes led to the silencing of endogenous genes in a homology-dependent manner ( Napoli et al. In the late 1980s and early 1990s, numerous studies demonstrated that expression of pieces of a viral genome in plants protected these plants from infection by the virus and even related viruses (reviewed in Prins et al. However, phenomena that can be at least partially attributed to small-RNA-mediated silencing were observed decades ago. The diversity and widespread existence of small RNAs and the fundamental importance of small-RNA-mediated regulation were not appreciated until recent years. Here I review the biogenesis and function of three major classes of endogenous small RNAs in plants: microRNAs, transacting siRNAs, and heterochromatic siRNAs, with an emphasis on the roles of these small RNAs in developmental regulation. Small RNAs are not only made from and target foreign nucleic acids such as viruses and transgenes, but are also derived from endogenous loci and regulate a multitude of developmental and physiological processes. Some small RNAs cause transcriptional gene silencing by guiding heterochromatin formation at homologous loci, whereas others lead to posttranscriptional gene silencing through mRNA degradation or translational inhibition. Many eukaryotic organisms have evolved multiple members of RNase III and the argonaute family of proteins to accommodate different classes of small RNAs with specialized molecular functions. Many, although not all, small RNAs are processed from double-stranded RNAs or single-stranded RNAs with local hairpin structures by RNase III enzymes and are loaded into argonaute-protein-containing effector complexes. Small RNAs of 20–30 nucleotides guide regulatory processes at the DNA or RNA level in a wide range of eukaryotic organisms.
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