A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis

Manabu Yoshikawa, Angela Peragine, Yeon Park Mee, R. Scott Poethig

Research output: Contribution to journalArticlepeer-review

601 Scopus citations


The Arabidopsis genes, TAS2 and TAS1a, produce structurally similar noncoding transcripts that are transformed into short (21-nucleotide [nt]) and long (24-nt) siRNAs by RNA silencing pathways. Some of these short siRNAs direct the cleavage of protein-coding transcripts, and thus function as trans-acting siRNAs (ta-siRNAs). Using genetic analysis, we defined the pathway by which ta-siRNAs and other short siRNAs are generated from these loci. This process is initiated by the miR173-directed cleavage of a primary poly(A) transcript. The 3′ fragment is then transformed into short siRNAs by the sequential activity of SGS3, RDR6, and DCL4: SGS3 stabilizes the fragment, RDR6 produces a complementary strand, and DCL4 cleaves the resulting double-stranded molecule into short siRNAs, starting at the end with the miR173 cleavage site and proceeding in 21-nt increments from this point. The 5′ cleavage fragment is also processed by this pathway, but less efficiently. The DCL3-dependent pathway that generates long siRNAs does not require miRNA-directed cleavage and plays a minor role in the silencing of these loci. Our results define the core components of a post-transcriptional gene silencing pathway in Arabidopsis and reveal some of the features that direct transcripts to this pathway.

Original languageEnglish (US)
Pages (from-to)2164-2175
Number of pages12
JournalGenes and Development
Issue number18
StatePublished - Sep 15 2005


  • PTGS
  • RNAi
  • Trans-acting siRNAs
  • miRNA


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