The evolutionary study of small RNA-directed gene silencing pathways by investigating RNase III enzymes

Lihua Jin, Kirill Kryukov, Yoshiyuki Suzuki, Tadashi Imanishi, Kazuho Ikeo, Takashi Gojobori*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


The RNA-mediated gene silencing pathways are evolutionarily conserved processes. They highlight a fundamental role of short RNAs in eukaryotic gene regulation and antiviral defense. Recently three distinct small RNA-directed silencing pathways are observed, such as the destruction of mRNA via siRNA, inhibition of mRNA translation via miRNA, and epigenetic gene silencing via siRNA. It was also found that in these pathways, the members of ribonuclease III family play important roles in diverse RNA maturation and decay. Here we investigated the evolution of RNase III nucleases, Dicer as representative, to further figure out the evolutionary relationship of these three gene silencing pathways. With the advantage of using genomic sequences as the subject in homolog search, in un-annotated genomic regions, we were able to detect possible candidates for 3 functional domains and genes of dicer and drosha. Moreover, we found that prokaryotes including eubacteria and archaea lack completely the PAZ domain of Dicer. These results show the taxonomic-dependent evolution of the RNA-mediated gene silencing pathways.

Original languageEnglish (US)
Pages (from-to)1-8
Number of pages8
Issue number1-2
StatePublished - Apr 15 2009
Externally publishedYes

Bibliographical note

Funding Information:
We greatly appreciate Takuro Tamura for the technical assistance. We give special thanks to Barrero Roberto and Yoshio Tateno for their insightful advices. This research was, in part, supported by the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology, Japan and by the BIRC (Biological Information Research Center) at AIST (National Institute for Advanced Industrial Studies and Technology).


  • Epigenetic gene silencing
  • Nuclease domain
  • PAZ domain
  • Posttranscriptional gene silencing
  • RNase III enzyme
  • Small-RNA guided gene silencing pathway

ASJC Scopus subject areas

  • Genetics


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