A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

Ruiqiang Ye, Zulong Chen, Bi Lian, M. Jordan Rowley, Ning Xia, Jijie Chai, Yan Li, Xin Jian He, Andrzej T. Wierzbicki, Yijun Qi

Research output: Contribution to journalArticlepeer-review

97 Scopus citations


DNA methylation directed by 24-nucleotide (nt) small interfering RNAs (siRNAs) plays critical roles in gene regulation and transposon silencing in Arabidopsis. 24-nt siRNAs are known to be processed from double-stranded RNAs by Dicer-like 3 (DCL3) and loaded into the effector Argonaute 4 (AGO4). Here we report a distinct class of siRNAs independent of DCLs (sidRNAs). sidRNAs are present as ladders of ~20-60 nt in length, often having the same 5' ends but differing in 3' ends by 1-nt steps. We further show that sidRNAs are associated with AGO4 and capable of directing DNA methylation. Finally we show that sidRNA production depends on distributive 3'-5' exonucleases. Our findings suggest an alternative route for siRNA biogenesis. Precursor transcripts are bound by AGO4 and subsequently subjected to 3'-5' exonucleolytic trimming for maturation. We propose that sidRNAs generated through this route are the initial triggers of de novo DNA methylation.

Original languageEnglish (US)
Pages (from-to)222-235
Number of pages14
JournalMolecular Cell
Issue number2
StatePublished - Jan 21 2016
Externally publishedYes

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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