Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17466-73. doi: 10.1073/pnas.1012891107. Epub 2010 Sep 24.


In Arabidopsis thaliana, four different dicer-like (DCL) proteins have distinct but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and siRNAs from longer, noncoding precursor RNAs. To analyze the impact of different components of the small RNA biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in small RNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. Our analysis revealed a surprising number of common targets in dcl1 and dcl2 dcl3 dcl4 triple mutants. Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism*
  • DNA Methylation
  • DNA Transposable Elements / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Plant / genetics
  • Gene Expression Regulation, Plant / physiology*
  • MicroRNAs / biosynthesis*
  • Mutation / genetics
  • Protein Array Analysis
  • Reverse Transcriptase Polymerase Chain Reaction
  • Ribonuclease III / genetics
  • Ribonuclease III / metabolism*


  • Arabidopsis Proteins
  • Cell Cycle Proteins
  • DNA Transposable Elements
  • MicroRNAs
  • DCL4 protein, Arabidopsis
  • DCL1 protein, Arabidopsis
  • DCL2 protein, Arabidopsis
  • DCL3 protein, Arabidopsis
  • Ribonuclease III

Associated data

  • GEO/GSE21685