Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs

Mol Cell. 2004 Oct 8;16(1):69-79. doi: 10.1016/j.molcel.2004.09.028.


Here we describe a set of endogenous short interfering RNAs (siRNAs) in Arabidopsis, some of which direct the cleavage of endogenous mRNAs. These siRNAs correspond to both sense and antisense strands of a noncoding RNA (At2g27400) that apparently is converted to double-stranded RNA and then processed in 21 nt increments. These siRNAs differ from previously described regulatory small RNAs in two respects. First, they require components of the cosuppression pathway (RDR6 and SGS3) and also components of the microRNA (miRNA) pathway (AGO1, DCL1, HEN1, and HYL1) but not components needed for heterochromatic siRNAs (DCL3 and RDR2), another class of endogenous plant siRNAs. Second, these siRNAs repress the expression of genes that have little overall resemblance to the genes from which they originate, a characteristic previously reported only for miRNAs. The identification of this silencing pathway provides yet another dimension to posttranscriptional mRNA regulation in plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Argonaute Proteins
  • Base Sequence
  • Cell Cycle Proteins
  • Gene Expression Regulation, Plant / physiology*
  • MicroRNAs / metabolism
  • Molecular Sequence Data
  • Mutation
  • RNA, Messenger / metabolism*
  • RNA, Small Interfering / metabolism*
  • RNA-Binding Proteins / metabolism
  • Ribonuclease III / metabolism
  • Sequence Analysis, DNA


  • AGO1 protein, Arabidopsis
  • Arabidopsis Proteins
  • Argonaute Proteins
  • Cell Cycle Proteins
  • HEN1 protein, Arabidopsis
  • HYL1 protein, Arabidopsis
  • MicroRNAs
  • RNA, Messenger
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • SGS3 protein, Arabidopsis
  • DCL1 protein, Arabidopsis
  • Ribonuclease III