Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis

Nucleic Acids Res. 2012 Jul;40(13):6241-54. doi: 10.1093/nar/gks242. Epub 2012 Mar 19.

Abstract

Biogenesis of trans-acting siRNAs (tasiRNAs) is initiated by miRNA-directed cleavage of TAS gene transcripts and requires RNA-dependent RNA polymerase 6 (RDR6) and Dicer-like 4 (DCL4). Here, we show that following miR173 cleavage the entire polyadenylated parts of Arabidopsis TAS1a/b/c and TAS2 transcripts are converted by RDR6 to double-stranded (ds)RNAs. Additionally, shorter dsRNAs are produced following a second cleavage directed by a TAS1c-derived siRNA. This tasiRNA and miR173 guide Argonaute 1 complexes to excise the segments from TAS2 and three TAS1 transcripts including TAS1c itself to be converted to dsRNAs, which restricts siRNA production to a region between the two cleavage sites. TAS1c is also feedback regulated by a cis-acting siRNA. We conclude that TAS1c generates a master siRNA that controls a complex network of TAS1/TAS2 siRNA biogenesis and gene regulation. TAS1/TAS2 short dsRNAs produced in this network are processed by DCL4 from both ends in distinct registers, which increases repertoires of tasiRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / metabolism*
  • Base Sequence
  • Gene Expression Regulation, Plant*
  • Gene Knockdown Techniques
  • Genes, Plant
  • MicroRNAs / metabolism
  • Molecular Sequence Data
  • Polyadenylation
  • RNA Cleavage
  • RNA Precursors / chemistry
  • RNA Precursors / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Double-Stranded / chemistry
  • RNA, Double-Stranded / metabolism*
  • RNA, Plant / chemistry
  • RNA, Plant / genetics
  • RNA, Plant / metabolism
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism*
  • RNA-Dependent RNA Polymerase / metabolism*

Substances

  • Arabidopsis Proteins
  • MIRN173 microRNA, Arabidopsis
  • MicroRNAs
  • RNA Precursors
  • RNA, Double-Stranded
  • RNA, Plant
  • RNA, Small Interfering
  • RDR6 protein, Arabidopsis
  • RNA-Dependent RNA Polymerase