Characteristics and processing of Pol IV-dependent transcripts in Arabidopsis

In plants, RNA-directed DNA methylation (RdDM) plays an essential role in silencing transposable elements that would otherwise have a deleterious effect on genome integrity. RdDM is an important pathway that establishes and maintains de novo DNA methylation in all three sequence contexts: CG, CHG, and CHH (where H is A, C, or T), and the methylation is targeted by 24-nt small interfering RNAs (siRNAs) (Law and Jacobsen, 2010). A plant-specific RNA polymerase (Pol IV) is required to initiate the production of 24-nt siRNAs by transcribing single-stranded RNA precursors at target loci (Law and Jacobsen, 2010; Matzke and Mosher, 2014). The precursors serve as templates for RNA-dependent RNA polymerase 2 (RDR2) to make double-stranded RNAs (dsRNAs), which are then cleaved by Dicer-like 3 (DCL3) into 24-nt siRNAs (Haag et al., 2012). Many studies were conducted to explore the biogenesis of 24-nt siRNAs; however, the nature of Pol IV precursor RNAs was unclear due to the rapid conversion into siRNAs (Li et al., 2015).