Abstract
Small RNA molecules can target a particular virus, gene, or transposable element (TE) with a high degree of specificity. Their ability to move from cell to cell and recognize targets in trans also allows building networks capable of regulating a large number of related targets at once. In the case of epigenetic silencing, small RNA may use the widespread distribution of TEs in eukaryotic genomes to coordinate many loci across developmental and generational time. Here, we discuss the intriguing role of plant small RNA in targeting transposons and repeats in pollen and seeds. Epigenetic reprogramming in the germline and early seed development provides a mechanism to control genome dosage, imprinted gene expression, and incompatible hybridizations via the "triploid block."
Highlights
From developmental signaling to virus resistance, small RNA molecules (sRNAs) have many important functions in plant cells, yet the majority of them target repeats and transposable elements (TEs) previously considered largely inert (Borges and Martienssen 2015)
In flowering plants, repeated regions and TEs typically produce small-interfering RNA molecules that are 23- to 24-nt-long, abundant 21-nt and 22-nt siRNAs are produced in some species or specific developmental contexts and are known as epigenetically activated siRNA (Nuthikattu et al 2013; Creasey et al 2014). easiRNA precursors can be transcribed by the RNA polymerase II (Pol II) or the plant-specific RNA polymerase IV, which shares many subunits with Pol II and is generally required for TE siRNA production
Pol IV generates short transcripts (Blevins et al 2015; Zhai et al 2015) that are immediately converted into double-stranded RNA by the RNA DEPENDENT RNA POLYMERASE2 (RDR2), which forms a complex with Pol IV and is required for polymerase activity (Singh et al 2019)
Summary
Epigenetic reprogramming refers to the erasure and resetting of epigenetic marks acquired during the life of the parent, and in mammals it occurs in the gametes and in the embryo (Heard and Martienssen 2014). How those epialleles are formed and how they acquire the ability to be propagated through cell divisions remains a tantalizing mystery, as DNA methylation seems to play only a minor role It has, been shown in Arabidopsis that some components of small RNA pathways are both required and sufficient to initiate de novo silencing of naive alleles (Fultz and Slotkin 2017; Gallego-Bartolomé et al 2019). IDN2 binds to long (10- to 11-nt) 5′ overhangs, presumably reflecting the cleaved RNA molecule still bound to the small RNA, and in turn recruits a variety of chromatin remodeling proteins responsible for silencing (Zhu et al 2013; Liu et al 2016), including DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) that methylates corresponding DNA in all sequence contexts (Böhmdorfer et al 2014). The activity of the DDR complex appears as a key to small RNA–guided epigenetic silencing
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