Catalytic RNA world relics in Dicer RNAs

Sayak Ganguli¹*, Dey S.K.², Priyanka Dhar³, Protip Basu⁴, Paushali Roy⁵, Abhijit Datta^6
1DBT-Centre for Bioinformatics, Presidency College, Kolkata
²DBT-Centre for Bioinformatics, Presidency College, Kolkata
³DBT-Centre for Bioinformatics, Presidency College, Kolkata
⁴DBT-Centre for Bioinformatics, Presidency College, Kolkata
⁵DBT-Centre for Bioinformatics, Presidency College, Kolkata
⁶DBT-Centre for Bioinformatics, Presidency College, Kolkata
* Corresponding Author : sayakbif@yahoo.com

Received : -     Accepted : -     Published : 15-06-2010
Volume : 2     Issue : 1       Pages : 8 - 17
Genetics 2.1 (2010):8-17
DOI : http://dx.doi.org/10.9735/0975-2862.2.1.8-17

Keywords : RNAi, Drosha, RISC, miRNA, ribozymes, motifs
Conflict of Interest : None declared
Acknowledgements/Funding : The authors are acknowledging the financial support from DBT, Govt. of India

RNA interference (RNAi) is a naturally occurring phenomenon of RNA-mediated gene silencing that is highly conserved among multicellular organisms. In the first step of the pathway, long doublestranded RNA molecules are chopped into shorter duplexes with 2 nucleotide overhangs at both 3’ ends by an endonuclease dubbed Dicer, the structure of which has been solved only recently. This results in the formation of small 21 nucleotide long RNAs, aptly named small or short interfering RNAs (siRNAs), which are incorporated into a multimeric protein complex, the RNA-induced silencing complex (RISC). One of the two-siRNA strands guides RISC to a complementary RNA. After hybridization the endonucleolytic “slicer” activity of RISC cleaves the target RNA, thus preventing its translation. While long double-stranded RNA molecules can be employed to induce RNAi in lower eukaryotes, siRNAs being 21 nucleotides in length have to be used for gene silencing in mammalian cells in order to prevent the activation of an unspecific interferon response [1]. In contrast to siRNAs, however, miRNAs are capable of inhibiting translation of the targeted mRNA without degrading it (at least in mammalian cells)[2-4]. The need for in silico analysis of the components of the RNA interference pathway arises from the fact that very little is known about the structural and interacting properties of the components. With the above background the analysis was performed to identify putative catalytic motifs in the mRNA of the DICER enzyme.