Data mining of imperfect double-stranded RNA in 3′ untranslated regions of eukaryotic mRNAs

Recent developments in the study of RNA silencing indicate that double-stranded RNA (dsRNA) can be used in eukaryotes to block expression of a corresponding cellular gene. There is also a large class of small non-coding RNAs having potential to form a distinct, stable stem-loop in numbers of eukaryotic genomes. We had reported that a large imperfect dsRNA structure with hundreds of base-pairs (bp) in the $3^{\prime }$ untranslated region ($3^{\prime }$UTR) of cytotoxic ribonuclease was correlated with the translation suppression. In this study, we search for such dsRNAs in a $3^{\prime }$ UTR database. The occurrence rate of large dsRNA in $3^{\prime }$ UTRs ranges from 0.01% in plant to 0.30% in vertebrate mRNAs. However, small imperfect dsRNAs of $\sim$ 30 bp are much more prevalent than large ones. The small dsRNAs are statistically very significant and uniquely well-ordered. Most of them have the conserved structural features of pre-miRNAs. Our data mining of the dsRNAs in the $3^{\prime }$ UTR database can be used to explore RNA-based regulation of gene expression.