![]() Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Purines are required at the 5′ ends of newly initiated RNAs for optimal RNA polymerase III gene expression. The nucleotide sequence of the initiation and termination sites for ribosomal RNA transcription in X. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Nascent RNA sequencing reveals distinct features in plant transcription. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Biochemical specialization within Arabidopsis RNA silencing pathways. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Genetic and functional diversification of small RNA pathways in plants. Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. These results highlight the importance of Pol V transcript slicing in RNA-mediated transcriptional gene silencing, which is a conserved process in many eukaryotes. We also found that Pol V transcript slicing required SUPPRESSOR OF TY INSERTION 5-LIKE (SPT5L), an elongation factor whose function is not well understood. Expression of wild-type AGO4 in ago4/6/9 mutants was able to restore slicing of Pol V transcripts, but a catalytically inactive AGO4 mutant did not correct the slicing defect. This uracil was complementary to the 5′ adenine found in many AGO4-bound 24-nucleotide siRNAs and was eliminated in a siRNA-deficient mutant as well as in the ago4/6/9 triple mutant, suggesting that the +10 U signature is due to siRNA-mediated co-transcriptional slicing of Pol V transcripts. We uncovered unique characteristics of Pol V RNAs, including a uracil (U) common at position 10. Here, we used a modified global nuclear run-on protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide. RdDM also requires non-coding RNAs transcribed by RNA polymerase V (Pol V) that probably serve as scaffolds for binding of AGO4–siRNA complexes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide small interfering RNAs (siRNAs) that bind to ARGONAUTE 4 (AGO4) and target genomic regions for silencing. Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes.
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