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The expanding world of small RNAs in plants
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The expanding world of small RNAs in plants
The expanding world of small RNAs in plants
Journal Article

The expanding world of small RNAs in plants

2015
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Overview
Key Points Functional diversification and expansion of silencing pathways in plants relies on duplication of DICER-LIKE proteins (DCLs) and ARGONAUTE proteins (AGOs). The main small-RNA classes in plants are microRNAs (miRNAs), 21–22-nucleotide secondary siRNAs and 24-nucleotide heterochromatic siRNAs (hetsiRNAs). All small RNAs in plants are modified at their 3′-end by 2′- O -methylation, including miRNAs, which lack this modification in animals. This modification confers stability and protection from degradation. Plant miRNAs are mainly involved in post-transcriptional gene silencing (PTGS) by transcript cleavage or translational repression, and also trigger secondary siRNA production from RNA polymerase II (Pol II) transcripts. Secondary small RNAs of 21 and 22 nucleotides in length are involved in cleavage or translational repression of target transcripts in cis and in trans . They are also able to initiate TGS by establishing DNA methylation at particular loci. The majority of siRNAs in plants are 24-nucleotide hetsiRNAs and are involved in silencing repeats and transposable elements by RNA-directed DNA methylation (RdDM). Small RNAs in plants are involved in reproductive transitions, including meiosis and gametogenesis, and regulate important epigenetic mechanisms such as genomic imprinting and paramutation. Plant genomes encode diverse small RNAs, such as microRNAs, secondary siRNAs, heterochromatic siRNAs and various RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins. Together, these constitute several genetic and epigenetic silencing pathways with diverse cellular and developmental functions, in processes including reproductive transitions, genomic imprinting and paramutation. Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.