Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer

Nucleic Acids Res. 2015 Dec 15;43(22):10939-51. doi: 10.1093/nar/gkv968. Epub 2015 Sep 30.

Abstract

The ribonuclease Dicer excises mature miRNAs from a diverse group of precursors (pre-miRNAs), most of which contain various secondary structure motifs in their hairpin stem. In this study, we analyzed Dicer cleavage in hairpin substrates deprived of such motifs. We searched for the factors other than the secondary structure, which may influence the length diversity and heterogeneity of miRNAs. We found that the nucleotide sequence at the Dicer cleavage site influences both of these miRNA characteristics. With regard to cleavage mechanism, we demonstrate that the Dicer RNase IIIA domain that cleaves within the 3' arm of the pre-miRNA is more sensitive to the nucleotide sequence of its substrate than is the RNase IIIB domain. The RNase IIIA domain avoids releasing miRNAs with G nucleotide and prefers to generate miRNAs with a U nucleotide at the 5' end. We also propose that the sequence restrictions at the Dicer cleavage site might be the factor that contributes to the generation of miRNA duplexes with 3' overhangs of atypical lengths. This finding implies that the two RNase III domains forming the single processing center of Dicer may exhibit some degree of flexibility, which allows for the formation of these non-standard 3' overhangs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • MicroRNAs / chemistry*
  • MicroRNAs / metabolism*
  • Nucleic Acid Conformation
  • RNA Cleavage
  • RNA Precursors / chemistry*
  • RNA Precursors / metabolism*
  • RNA-Binding Proteins / metabolism
  • Ribonuclease III / metabolism*

Substances

  • MicroRNAs
  • RNA Precursors
  • RNA-Binding Proteins
  • trans-activation responsive RNA-binding protein
  • Ribonuclease III