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Fig. 3 | Genome Biology

Fig. 3

From: Evolution of plant genome architecture

Fig. 3

The role of small RNAs in plant genome evolution. a Plant genomes are rich sources of small RNAs, which are predominantly the products of three major pathways. (1) Heterochromatic siRNAs (hc-siRNAs) are 24-nucleotide products of the activity of the plant-specific Pol IV and Pol V pathways; hc-siRNAs derive from heterochromatic regions and target those regions for reinforcement of silencing chromatin marks. (2) MicroRNAs (miRNAs) are ~21-nucleotide or 22-nucleotide products of processed long noncoding mRNAs that function to suppress target mRNAs either by (2a) blocking translation, or (2b) directing Argonaute-mediated slicing of targets. Plant miRNAs typically function by directing slicing. (3) Some miRNAs, typically 22 nucleotides long, trigger the production of secondary siRNAs, which are products of DCL4 and are 21 nucleotide long, from their target mRNAs. This pathway requires RDR6, and some resulting siRNAs can act in trans to slice additional targets; hence their name of trans-acting siRNAs (tasiRNAs). b hc-siRNAs are typically derived from TEs, the predominant component of inactive chromatin in plant genomes. Transposons (colored parallelograms in 1–3) can be silenced (blue triangles) as a result of RNA-directed DNA methylation mediated by hc-siRNAs derived from those elements (thin blue arrows). Some transposons can escape DNA methylation and silencing (white dots), to later remobilize. Transposons can be additionally silenced by hc-siRNAs functioning in trans from related TEs (dashed lines). After allopolyploid individuals form (2), the genomic context changes for TEs from the progenitor genomes, and these elements can be silenced by hc-sRNAs derived from sequence-similar TEs residing in the added genome (dashed, curvy lines). After this period of adaptation (3), some TEs can be newly silenced (gold triangles), whereas a few might remain unsilenced and active, and might amplify into the added genome (thin black arrows). UTR untranslated region

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